data/sams/filtered.json

{
  "21785141": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/21785141.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the protein AtFib2, which is a form of fibrillarin, and details the methods used for protein expression in E. coli, including the use of IPTG for induction and purification techniques involving Ni-NTA agarose. Furthermore, the paper describes an in vitro enzymatic assay, specifically an electrophoretic mobility shift assay (EMSA), to measure the RNA-binding activity of the purified AtFib2 protein and its mutants. This combination of protein purification and enzymatic activity measurement is characteristic of experimental enzymology studies.\n",
        "doc_id": "a1d00e0b-2b44-46f7-a8a5-a44f4509cbdb"
      }
    ]
  },
  "17643375": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/17643375.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the BCDIN3 enzyme on the 7SK snRNA, which is a clear indication of an enzymatic assay. The paper describes the incubation of recombinant 7SK snRNA with His-tagged BCDIN3 and 3H-AdoMet, and the detection of the methylated RNA product through autoradiography. Additionally, it mentions the purification of BCDIN3 and its role in the methylation process, which aligns with the typical structure of experimental enzymology papers that include protein overexpression, purification, and enzymatic activity assays.\n",
        "doc_id": "bc6a1d5b-04dc-49ef-9e24-6b8674e34329"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the BCDIN3 protein, which is indicated by the mention of \"His-tagged BCDIN3 expressed and purified from bacteria.\" Additionally, the paper describes in vitro enzymatic assays to measure the activity of the purified enzyme, specifically the methylation of 7SK snRNA by BCDIN3 in the presence of radiolabeled AdoMet, and the effects of various treatments on this activity. The use of assays to confirm the enzymatic nature of the reaction and the restoration of activity upon addition of recombinant BCDIN3 further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "89ffd352-82e6-41c5-be1b-149eff29f878"
      }
    ]
  },
  "18757072": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/18757072.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. The authors discuss the expression and purification of the YFV NS5 protein, which is a methyltransferase, and they describe the use of mass spectrometry to analyze its phosphorylation sites and enzymatic activity. Specifically, they mention that the hydroxyl group of serine 56 is required for 2′-O methylation in vitro, indicating that they are measuring the enzymatic activity of the purified enzyme. The methods section details the transfection of HEK293T cells, purification of the protein using metal affinity chromatography, and subsequent analysis, which aligns with the typical characteristics of experimental enzymology papers.\n",
        "doc_id": "a9315770-e7e0-4b0d-a8da-3c74739a21d7"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the YFV NS5 methyltransferase enzyme, as well as the performance of in vitro methylation assays to measure the enzymatic activity of both wild-type and mutant forms of the enzyme. The paper details the methods used for protein purification, the enzymatic assays conducted to assess the effects of specific mutations on methyltransferase activity, and the analysis of the products via thin layer chromatography. These elements are characteristic of experimental enzymology studies, which focus on the functional analysis of enzymes.\n",
        "doc_id": "040f57f8-ecca-4aff-bf7a-1ee22420f0d1"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the YFV NS5 proteins and methyltransferase domain in HEK293T and E. coli cells, respectively. The methods section details the transfection of cells, the use of Ni-NTA magnetic agarose beads for protein purification, and the enzymatic assays involving the binding of the purified proteins to SAH-labeled Sepharose. The paper also describes the use of mass spectrometry to analyze the proteins, which is common in enzymology studies to confirm the identity and activity of the enzymes. Overall, the focus on protein expression, purification, and subsequent assays indicates that this paper fits well within the realm of experimental enzymology.\n",
        "doc_id": "bcf47967-55b2-4b77-8389-84cf89a9c9ac"
      }
    ]
  },
  "10779558": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/10779558.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Gcd10p-Gcd14p complex, which is identified as a tRNA(m1A) methyltransferase. The paper details the enzymatic activity of the purified complex, including kinetic analysis that provides KM values for the substrates involved. It also mentions the use of S-adenosylmethionine (AdoMet) as a methyl donor in the enzymatic reaction, which is a key aspect of experimental enzymology. The methods section indicates that the authors performed in vitro assays to measure the activity of the purified enzyme, which is a hallmark of experimental enzymology studies.\n",
        "doc_id": "6310c200-2dab-4f0d-b46d-586c7280d6c4"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins (e.g., Gcd10p and Gcd14p) and includes detailed methods for affinity purification of these proteins from yeast extracts. Additionally, it describes in vitro enzymatic assays to measure the activity of the purified enzyme complexes, specifically mentioning MTase activities and the use of radiolabeled substrates to quantify the enzymatic reactions. The presence of these elements indicates that the paper focuses on experimental enzymology.\n",
        "doc_id": "23da3f6a-5671-469a-8670-887ddba6d172"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the FlagGcd10p-Gcd14p complex and its enzymatic activity as a tRNA(m1A) methyltransferase (MTase). The paper details the purification process, including the use of Flag affinity resin and gel filtration, and describes in vitro assays to measure the enzyme's activity in transferring a radiolabeled methyl group to tRNA. The results section specifically mentions the MTase activity of the purified complex, indicating that the authors conducted enzymatic assays to assess the function of the enzyme, which is a hallmark of experimental enzymology.\n",
        "doc_id": "b9fcaf0f-b068-4a3d-aadc-8dac88911b8f"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification of the FlagGcd10p/Gcd14p complex and its enzymatic activity as a tRNA(m¹A)MTase. The paper details the measurement of initial reaction velocities to calculate Kₘ values for AdoMet and tRNAᴹᵉᵗ, indicating that in vitro enzymatic assays were performed to assess the activity of the purified enzyme. Additionally, it describes the introduction of mutations to study their effects on enzyme function, which is a common approach in experimental enzymology to understand enzyme mechanisms and activity.\n",
        "doc_id": "b0bba49d-0eff-4bab-83c8-cc317f8eb52e"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the proteins Gcd14p and Gcd10p, and it describes in vitro enzymatic assays to measure the (m¹A)MTase activity of the purified Gcd14p/Gcd10p complex. The paper provides specific details about the assay methods used to evaluate enzyme activity, including the quantification of methylation of tRNA substrates and the requirement of Gcd10p for tRNA binding and enzyme activity. The results demonstrate the enzymatic function of the purified complex, which is a hallmark of experimental enzymology studies.\n",
        "doc_id": "769ed3d9-56f0-4f1e-9d6a-2c52d35cc317"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the Gcd10p and Gcd14p proteins and their roles in tRNA modification, specifically mentioning the (m¹A)MTase activity of the Gcd10pyGcd14p complex. The text indicates that the authors performed experiments to assess the enzymatic activity of the purified proteins, including the observation that purified Gcd14p alone had no (m¹A)MTase activity and that the complex's ability to bind tRNA substrates was affected by the presence of Gcd10p. This focus on protein purification and enzymatic assays aligns well with the characteristics of experimental enzymology papers.",
        "doc_id": "a7017e82-6625-454d-8d44-cf770f5461b3"
      }
    ]
  },
  "22308031": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/22308031.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the methylation activity of the KsgA enzyme on the 30S ribosomal subunit, including details about the in vitro methylation assays used to study the enzyme's activity. The paper mentions the isolation of non-methylated 30S subunits and their conversion into a methylation-competent conformation, which indicates that enzymatic assays were performed to measure the activity of KsgA. Additionally, it describes the effects of specific mutations on the enzyme's activity, further supporting its focus on experimental enzymology.\n",
        "doc_id": "ec57a730-9270-43f3-9446-281b1ecf1659"
      }
    ]
  },
  "27629654": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/27629654.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme PaTrm5a, as well as its enzymatic activity, specifically mentioning in vitro activity assays that demonstrate the methylation reactions catalyzed by this enzyme. The paper details the structural analysis of the enzyme and its interactions with substrates, which are key components of experimental enzymology.\n",
        "doc_id": "14e2d9bc-add0-452e-8831-b5e499b85179"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The Methods section describes the cloning, expression, and purification of the enzyme PaTrm5a, which is a key aspect of experimental enzymology. It details the use of E. coli for overexpression, the purification process using Ni-NTA affinity chromatography, and the treatment with RNase A to remove nucleic acids. Additionally, the paper mentions the preparation of crystallization samples with the purified enzyme, indicating that the authors are investigating the enzyme's structure and potentially its activity. The focus on the enzyme's conformation and its implications for function further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "2625875b-6c5c-4121-8da2-5afabc058cc2"
      }
    ]
  },
  "36546776": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/36546776.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the cloning, expression, and purification of the NSP14 protein, which is a key enzyme involved in the capping of viral RNA. The Methods section details the overexpression of NSP14 in E. coli, the purification process using various chromatography techniques, and the preparation of the protein for future experiments. Although the paper does not explicitly mention an in vitro enzymatic assay to measure the activity of the purified enzyme, the focus on protein purification and the context of studying enzymatic functions suggest that it is part of an experimental enzymology study aimed at understanding the enzymatic properties of NSP14.\n",
        "doc_id": "17be5484-65b6-44aa-ad83-610e22fa9384"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins (NSP10 and NSP14) and describes methods for enzymatic assays, such as limited proteolysis and mass spectrometry analysis to assess the activity and characteristics of the purified proteins. The detailed methodology for protein purification, including the use of GST resin and dialysis, indicates a focus on enzymatic activity measurement, which is a hallmark of experimental enzymology.\n",
        "doc_id": "2cae3156-1e4b-4840-8848-5764284c99e7"
      }
    ]
  },
  "21045305": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/21045305.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a protein (TehB) and details the methods used for these processes, including the use of a His-Trap column for purification and the analysis of the purified protein by SDS-PAGE. The paper also mentions the use of crystallization techniques, which are often employed in enzymology to study the structure of enzymes, although it does not explicitly describe an in vitro enzymatic assay to measure the activity of the purified enzyme. However, the focus on protein purification and characterization aligns with the typical content of experimental enzymology papers.\n",
        "doc_id": "16c1b9b5-81a4-4cec-976f-268f94d9739d"
      }
    ]
  },
  "20424163": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/20424163.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme protein L-isoaspartyl methyltransferase (PIMT) and includes detailed methods for recombinant protein expression in Escherichia coli, as well as purification steps using glutathione-Sepharose resin. The paper also describes the enzymatic activity of PIMT in repairing isoaspartates, which indicates that in vitro enzymatic assays are likely involved in measuring the activity of the purified enzyme. The mention of the enzyme's mechanism and its role in protein damage repair further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "5114f8a2-e626-4dfc-aaf4-2dd540db647e"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the protein GST-PIMT, which is a methyltransferase enzyme, and describes an in vitro enzymatic assay to measure its activity. The methods section details the incubation of recombinant GST-PIMT with substrates and the use of tritiated AdoMet to assess the enzyme's activity, indicating that the paper focuses on experimental enzymology. Additionally, the results section provides evidence of the enzyme's functional activity, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "87ded777-e192-4b56-9f0e-5eac5a90c22b"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the protein GST-PIMT, which is a methyltransferase enzyme. The methods section describes how the protein was expressed in E. coli, purified using glutathione-Sepharose resin, and then subjected to enzymatic assays to measure its activity in transferring methyl groups from AdoMet to isoaspartyl residues. The paper includes details about the experimental setup, including incubation conditions and the use of SDS-PAGE for analysis, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "49378737-4fb3-4071-89ab-2bf10f499ddf"
      }
    ]
  },
  "26470919": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/26470919.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The Methods section describes the expression and purification of the m1A58 methyltransferase (MTase) protein, detailing the use of E. coli for protein expression, the lysis of cells, and the purification process using a HisTrap Ni-NTA column. Additionally, it mentions the in vitro transcription of tRNA, which indicates that the authors are preparing substrates for enzymatic assays. The focus on the enzyme's activity and specificity, as well as the structural analysis of the enzyme-substrate complex, further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "1ba33ebe-d985-4b9a-ba9b-0a3d64fe997d"
      }
    ]
  },
  "10899996": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/10899996.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the catalytic mechanisms of RNA m5C methyl transferases, including the identification of specific cysteine residues as catalysts. The Methods section mentions the use of plasmids for the preparation of enzymes and the purification of T7 RNA polymerase, which indicates that there is a focus on the overexpression and purification of proteins. Additionally, the paper describes biochemical studies and mechanisms of enzymatic activity, which are key components of experimental enzymology. The mention of substrate analogs and the characterization of enzyme-substrate interactions further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "2a41aaee-3e2a-4a25-94d0-4976da8dcffd"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of the enzyme Fmu, including the overexpression of Fmu mutants and their purification through various chromatography techniques. The paper also describes in vitro enzymatic assays to measure the activity of the purified enzyme, specifically detailing a methylation assay involving 16S rRNA and the use of [³H-Me]AdoMet as a methyl donor. The presence of these experimental methods and enzymatic assays clearly indicates that this paper falls within the realm of experimental enzymology.\n",
        "doc_id": "a86f0226-860b-41ec-8045-27f4b7e7bcb7"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the preparation of Cys-to-Ala mutations in the enzyme Fmu, the binding assays conducted to measure the interaction of these mutants with RNA substrates, and the catalytic activity of the mutants compared to the wild-type enzyme. Specifically, it mentions the enzymatic activity of the Cys325Ala mutant, which shows one-third to one-fourth the activity of the wild-type enzyme, indicating that the paper involves the study of enzyme function and activity, which is a key aspect of experimental enzymology. Additionally, the paper describes the purification and characterization of the enzyme, which aligns with the typical methods used in experimental enzymology studies.",
        "doc_id": "acbc38e9-37a6-4fbf-9b1d-0eee24bcd440"
      }
    ]
  },
  "2142454": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/2142454.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of non-structural proteins from Sindbis virus, specifically focusing on the proteinase activity of nsP2 and its role in polyprotein processing. The paper mentions the use of cell-free translation systems to study the proteolytic activity of nsP2-containing polyproteins, which indicates that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. Additionally, it describes the effects of specific mutations on cleavage site preferences, further emphasizing the experimental approach to understanding enzyme function.\n",
        "doc_id": "3b625305-95d0-4351-9117-327e00df140b"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the construction of cDNA clones for the expression of nsP2-containing polyproteins, which are then transcribed and translated in vitro. The paper details the use of these proteins in trans-cleavage assays to study their enzymatic activities, indicating that the authors are measuring the activity of the purified enzyme. The mention of in vitro transcription and translation, as well as the analysis of enzymatic activity through assays, aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "92fe3683-a2c6-45b4-80ab-472504e23c5b"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of non-structural polyproteins (nsP2, nsP3, etc.) and describes in vitro trans-cleavage assays to measure the enzymatic activity of these proteins. The methods section includes details about the synthesis of the proteins, the use of [35S]methionine for labeling, and the analysis of cleavage products using SDS-PAGE, which are all characteristic of experimental enzymology studies. The paper focuses on the enzymatic activity of the purified proteins and their ability to cleave specific sites, which aligns with the definition of experimental enzymology.\n",
        "doc_id": "79ce976d-4b67-419d-bb84-0363bc27bd2a"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the proteolytic activities of nsP2-containing polyproteins and mentions the use of in vitro techniques to study these activities. The paper describes the cleavage of polyprotein precursors and the specific sites involved, indicating that enzymatic assays were performed to measure the activity of the purified enzyme. Additionally, it references the use of mutagenesis and cell-free translation, which are common methods in experimental enzymology to analyze enzyme function and activity.\n",
        "doc_id": "90ec1025-3fe4-43d7-8855-ba39c0c3fffc"
      }
    ]
  },
  "25737013": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/25737013.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the in vitro methylation assays performed with the enzyme PRMT9 and its interaction with the substrate SAP145. The paper details the overexpression of PRMT9 in insect cells and the subsequent assays to measure its methylation activity on different fragments of SAP145, indicating a clear focus on enzymatic activity and purification methods. The mention of a catalytically inactive form of PRMT9 and the results from the methylation assays further support its classification as an experimental enzymology paper.\n",
        "doc_id": "5a86ce2e-4ec0-4d54-8015-bb3e7cb63478"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the PRMT9 protein, as indicated by the TAP-tag purification method described in the text. The paper also details an in vitro enzymatic assay where PRMT9 catalyzes the formation of methylated products (MMA and SDMA) in the presence of the SAP145 fragment, demonstrating the enzyme's activity. Additionally, the paper includes experiments that confirm the specificity of PRMT9 for certain residues and describes the conditions under which the enzyme is active, which are typical features of experimental enzymology studies.\n",
        "doc_id": "07c1700a-a460-46ce-9dbf-69b3e5a83db4"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins, specifically mentioning the generation of GST fusion proteins and the use of recombinant SAP145 in enzymatic assays. The paper describes the testing of various PRMTs for their ability to methylate SAP145, indicating that in vitro enzymatic assays were performed to measure the activity of these enzymes. Additionally, it details the use of a methyl-specific antibody to confirm methylation, which is a common approach in enzymology to assess enzyme activity. Overall, the focus on protein interactions and enzymatic activity aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "6283d721-b42b-40c1-a5f7-aff22f338fba"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the enzyme PRMT9 on the substrate SAP145, detailing the overexpression and purification of the recombinant HA-PRMT9 protein from Sf21 cells. The paper describes various experimental methods, including the use of western blotting, amino acid analysis, and thin-layer chromatography (TLC) to measure the enzymatic activity and confirm the methylation of specific arginine residues. The presence of these enzymatic assays and the focus on enzyme-substrate interactions clearly indicate that this is an experimental enzymology paper.\n",
        "doc_id": "f6eef8dc-8619-4f9b-aa87-c33a0fb2f8b8"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation assay performed using recombinant HA-PRMT9 as the enzyme and various substrates (GST-tagged SAP145 fragments). The paper details the methods used to assess the enzymatic activity, including the use of methylation-specific antibodies and western blotting to detect the methylation of SAP145, which indicates the measurement of enzyme activity. The mention of overexpression and purification of the enzyme, as well as the in vitro assay to measure its activity, aligns with the characteristics of experimental enzymology.\n",
        "doc_id": "1641582e-377e-44c0-9cb2-97672ab54f3d"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The Methods section describes the overexpression and purification of the PRMT9 protein using various vectors and systems, including the Baculovirus expression system. It also mentions the use of in vitro methylation assays to measure the activity of the purified enzyme, which is a key characteristic of experimental enzymology papers. The detailed description of the purification process and the enzymatic assay indicates that the study focuses on the enzymatic activity of the protein, aligning it with the criteria for experimental enzymology.\n",
        "doc_id": "296ab31a-1224-4260-a11a-080f9f08f15b"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It includes detailed descriptions of in vitro methylation assays, where recombinant enzymes and substrates are used to measure enzymatic activity. Specifically, the paper mentions the setup of methylation reactions, the use of S-adenosyl-l-[methyl-3H]methionine, and the subsequent analysis of the reaction products using techniques like SDS-PAGE and high-resolution cation-exchange chromatography. These elements indicate that the paper focuses on the overexpression, purification, and activity measurement of enzymes, which are key components of experimental enzymology.\n",
        "doc_id": "8bed8191-5e2b-460b-a827-dcf6d7fb1fd6"
      }
    ]
  },
  "31031083": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31031083.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methyltransferase assay performed to confirm that pri-let-7e is directly methylated by METTL1, which involves the use of a recombinant METTL1/WDR4 complex and specific substrates. The paper also describes the use of cellular extracts in an in vitro assay to test the efficiency of processing pri-let-7e into precursor and mature miRNAs, indicating a focus on enzymatic activity and the role of METTL1 in this process. These details point to the experimental enzymology nature of the research, as it involves the purification and functional analysis of an enzyme.\n",
        "doc_id": "dc2276f1-003b-44b0-b32f-b2cdf6899a54"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation reaction using recombinant METTL1/WDR4, which indicates the overexpression and purification of the enzyme METTL1. The paper also describes an in vitro processing assay of pri-let-7e, where the activity of the methylated pri-miRNAs is measured in the presence of immunoprecipitated DROSHA, demonstrating the enzymatic activity of the processed product. These details point to a clear focus on experimental enzymology, including the purification of enzymes and the measurement of their activity through specific assays.\n",
        "doc_id": "c4e4d768-eb13-4432-9e32-6e76bb21571b"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the expression and purification of recombinant METTL1/WDR4 and includes in vitro RNA methylation assays, which are key components of experimental enzymology. The mention of \"Expression and purification of recombinant METTL1/WDR4\" indicates that the authors have worked on isolating a specific enzyme, and the \"In vitro RNA methylation assays\" suggests that they have conducted enzymatic assays to measure the activity of this enzyme. These elements align well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "f7c67c4d-418f-41ab-903b-e3d853e88b92"
      },
      {
        "page": 20,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of the METTL1 enzyme, including details about the cloning of the METTL1 and WDR4 constructs into plasmids and the production of recombinant virus in insect cells. Additionally, it mentions the use of in vitro assays, such as the luciferase assay, to measure the activity of the METTL1 enzyme, which is a key component of experimental enzymology. The paper also describes the generation of a catalytically inactive METTL1 variant, indicating a focus on the enzyme's functional properties.\n",
        "doc_id": "521da61f-0877-441e-b998-536426e3235b"
      },
      {
        "page": 21,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of a protein/enzyme (specifically METTL1/WDR4) and includes details about in vitro enzymatic assays to measure the activity of the purified enzyme, such as the RNA methylation assays. The methods section describes the purification process using Ni-affinity and size-exclusion chromatography, as well as the subsequent enzymatic assays that involve incubating the enzyme with substrates to assess its activity. This aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "5aa966e7-1dca-45e5-a682-48819541bbef"
      }
    ]
  },
  "28196534": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28196534.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 35,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the growth of Aspergillus strains and includes specific details about enzyme assays, such as the measurement of laccase activity in the culture supernatant. The paper describes the conditions under which the strains were grown and the methods used to analyze enzyme activity, which are key components of experimental enzymology. Additionally, it mentions the purification and characterization of enzymes, indicating a focus on enzymatic assays to measure enzyme activity.\n",
        "doc_id": "bada50f6-2b9e-471f-8afb-5e83943581c2"
      },
      {
        "page": 36,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the determination of cellobiose dehydrogenase (CDH) activity using an in vitro enzymatic assay, where the decrease in absorption of DCPIP is monitored to measure enzyme activity. The methods section includes details about the substrate used, the conditions under which the assay is performed (temperature, pH, and buffer), and the specific absorbance measurements taken, which are all characteristic of experimental enzymology studies.\n",
        "doc_id": "84966134-6725-412d-bce6-5e0c7a20810a"
      }
    ]
  },
  "29983320": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/29983320.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 17,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of recombinant wild-type and D135S AlkB proteins, detailing the methods used for protein expression in BL21 bacteria and subsequent purification using Ni-NTA Agarose. Additionally, the paper describes in vitro enzymatic assays where the purified AlkB proteins are used to treat small RNAs to remove methylations, indicating the measurement of enzymatic activity. The specific conditions and components of the demethylation reaction are provided, which is characteristic of experimental enzymology studies.\n",
        "doc_id": "11351a5d-41b5-4817-9bc5-427adc06a703"
      }
    ]
  },
  "18982304": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/18982304.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the biochemical genomics approach that involves the preparation of purified proteins and the subsequent biochemical assay of these proteins to identify enzymatic activities. The mention of specific enzymes, such as methyltransferases and their roles in RNA modification, indicates that the paper focuses on enzymatic activities. Additionally, the inclusion of materials for enzymatic assays, such as radiolabeled tRNA substrates and various enzymes for RNA production, further supports the classification of this paper as an experimental enzymology study.\n",
        "doc_id": "b05a8792-1b77-4bdc-a014-79271b1c72a3"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of proteins from a GST-ORF library, which involves the overexpression and purification of enzymes. The mention of biochemical assays to detect interactions with RNA and the use of specific buffers and reagents for enzymatic reactions indicates that the paper is focused on experimental enzymology, particularly in the context of studying modifying enzymes. The detailed methods for protein purification and the mention of enzymatic assays further support this classification.\n",
        "doc_id": "104c9d07-6dcc-4d18-9300-898479bc6304"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the development of an activity assay for m1G37 methyltransferase, which involves the preparation of a radiolabeled tRNA substrate and the use of yeast crude extract to measure the enzyme's activity. The paper details the steps taken to perform the methyltransferase reactions, including the incubation of the substrate with the crude extract and the subsequent analysis of the reaction products using TLC. This indicates that the paper includes both the purification of the enzyme and an in vitro enzymatic assay to measure its activity, which are key components of experimental enzymology.\n",
        "doc_id": "5d751128-4cf6-4048-a23b-fc3f58a49392"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the assay for m1G37 methyltransferase activity, detailing the methods for measuring this enzymatic activity using a substrate tRNA and various reagents. The paper includes specific steps for preparing reactions, using RNase T2 for digestion, and employing thin-layer chromatography (TLC) to resolve and visualize the products of the enzymatic reaction. The mention of crude extracts and the conditions under which the enzymatic activity is measured indicates a focus on experimental enzymology.\n",
        "doc_id": "66e64df0-0a79-4ebe-8c35-a6adfd99cad8"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the assay for m1G37 methyltransferase activity, detailing the use of yeast crude extract as a source of enzymatic activity and describing the steps taken to identify the protein of interest through a biochemical genomics approach. The mention of performing assays with decreasing concentrations of crude extract and the specific focus on measuring the activity of the m1G37 methyltransferase indicates that the paper involves the purification and activity measurement of an enzyme, which is characteristic of experimental enzymology.\n",
        "doc_id": "673c87ad-3890-4afd-938c-829f7c1fcdbe"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins from a library of GST-ORF fusion proteins, specifically mentioning the identification of a methyltransferase activity associated with the Trm5 protein. The paper describes a method for assaying the enzymatic activity of these purified proteins, indicating that it involves in vitro enzymatic assays to measure the activity of the enzymes. The detailed approach to purifying and testing the proteins for specific enzymatic activities aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "84ab89c0-af6f-4057-aa17-80667cc0deda"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the assay of a GST-ORF library to identify the Trm5 protein, which is involved in the methylation of tRNA. The text mentions the use of a standard methyltransferase protocol to assay the activity of the protein, indicating that an enzymatic assay is being performed to measure the activity of the purified enzyme. Additionally, it describes the process of purifying the individual protein and cloning the identified open reading frame (ORF), which are key components of experimental enzymology.\n",
        "doc_id": "312591d9-fe4b-4df4-92a8-b245a43b2c34"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of proteins from Escherichia coli to assess their catalytic activity, which is a key aspect of experimental enzymology. The mention of using a uniformly labeled RNA substrate for enzymatic assays and the detailed description of assay procedures, including the use of TLC systems to visualize modified nucleotides, indicates that the paper involves in vitro enzymatic assays to measure the activity of the purified enzymes. This aligns well with the typical characteristics of experimental enzymology papers.\n",
        "doc_id": "93b646c3-5d48-4a20-9ed2-be8fafb0f0a5"
      }
    ]
  },
  "10917600": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/10917600.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the human coronavirus 229E helicase protein (p66ᴴᴱᴸ) using baculovirus vectors in insect cells, which is a key aspect of experimental enzymology. Additionally, the paper details the in vitro ATPase activity of the purified recombinant protein and its duplex-unwinding activities, indicating that enzymatic assays were performed to measure the activity of the enzyme. The mention of specific substrates and the conditions required for effective unwinding further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "6aee51bb-6bc2-4882-9cbe-197d8fba2f01"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the expression and purification of the recombinant HCoV helicase protein using a baculovirus expression system, which is a key aspect of experimental enzymology. The paper also details the purification process, including the use of His-tagged proteins and nickel-charged agarose, which are common techniques in enzymology studies. Furthermore, it mentions the examination of the NTPase activity of the helicase, indicating that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. This combination of protein purification and enzymatic activity measurement aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "317c7100-1b7c-4832-ac09-7721e5a96fb7"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the HEL and HEL-KA proteins from insect cells, which indicates the overexpression and purification of a protein/enzyme. The paper also details in vitro enzymatic assays measuring the ATPase and GTPase activities of the purified HEL protein, demonstrating its enzymatic function and the effects of different polynucleotides on its activity. The presence of specific data on enzyme activity and the conditions under which these assays were performed further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "5aecafa1-cd79-483e-b307-443fe2932ba3"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the RNA duplex-unwinding activity of the HEL protein and describes a standard helicase assay used to measure this activity. The paper details the experimental setup, including the use of partially double-stranded RNA substrates and the requirement of ATP for the helicase activity, which indicates an in vitro enzymatic assay. Additionally, it mentions the effects of different substrates on the activity of HEL and compares the activity of the wild-type protein with an ATPase-deficient variant, further emphasizing the experimental approach to studying enzyme function.\n",
        "doc_id": "52521d99-2096-4e43-891e-1650330035c2"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the unwinding activity of the HEL protein on various DNA and RNA substrates, indicating that the authors performed in vitro enzymatic assays to measure the activity of the HEL enzyme. Specifically, it mentions the conditions under which the enzyme unwinds duplex RNA and DNA, and it provides details about the experimental setup, including the use of different substrates and the amounts of enzyme used in the reactions. This aligns with the characteristics of experimental enzymology, which typically involves the purification and activity measurement of enzymes.\n",
        "doc_id": "eefcb0cb-cbe1-4f0a-b5f7-eae5d4aa3c5f"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the DNA duplex-unwinding activity of the HEL protein, which is a helicase, and describes experiments that involve incubating the HEL protein with various DNA substrates to measure its activity. The paper details the conditions under which the enzymatic reactions were performed, including the amounts of protein and substrates used, and it analyzes the results of these reactions to draw conclusions about the enzyme's activity and substrate preferences. This focus on the enzymatic assay and the characterization of enzyme activity aligns well with the criteria for an experimental enzymology paper.\n",
        "doc_id": "e1bfb7a8-2796-4c71-b77a-fb435bd0b7eb"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the identification and characterization of the HCoV p66ᴴᴱᴸ protein as an SF1 RNA helicase, including its biochemical properties and the specific enzymatic activity of unwinding RNA duplexes. The mention of \"RNA duplex-unwinding activity\" and the experimental setup involving reactions with varying amounts of the helicase protein (HEL) indicates that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. Additionally, the paper describes the methodology used to analyze the reactions, which is typical of experimental enzymology studies.\n",
        "doc_id": "79023b3b-ccc5-425c-8f21-359d8779d281"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the unwinding activity of a helicase enzyme (HEL) and includes details about the experimental setup, such as the use of DNA substrates and the analysis of reactions on polyacrylamide gels. The mention of ATPase activity stimulation by nucleic acids indicates that there are enzymatic assays being performed to measure the activity of the helicase, which is a key characteristic of experimental enzymology papers.\n",
        "doc_id": "7f62007b-1165-409f-8a05-821b6bb82147"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The Methods section describes the construction of baculovirus recombinants for the overexpression of the HCoV helicase, detailing the PCR amplification of the coding sequence and the subsequent cloning into a vector. It also mentions the infection of insect cells with recombinant baculovirus for protein expression and purification, which is a key aspect of experimental enzymology. Furthermore, the paper discusses the biochemical analysis of the helicase activity, indicating that in vitro assays were performed to study the enzyme's function, which aligns with the typical focus of experimental enzymology papers on enzyme activity measurement.\n",
        "doc_id": "ed576a96-ae2d-4b90-971d-9bd0e1526d63"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a protein/enzyme, specifically mentioning the use of ProBond affinity chromatography for the purification of His-tagged proteins. The methods section describes the steps taken to purify the enzyme, including the use of buffers and conditions for elution, which are typical in experimental enzymology studies. Additionally, the paper outlines the preparation of RNA and DNA substrates, which suggests that enzymatic assays may follow to measure the activity of the purified enzyme, although the specific assays are not detailed in the provided text.\n",
        "doc_id": "b50a6462-8bd3-4ded-a752-060c27631421"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and activity assays of enzymes, specifically mentioning the use of a duplex-unwinding assay and an ATPase assay. The methods section describes the incubation of the enzyme (HEL or HEL-KA) with substrates and the conditions under which these assays are performed, including the use of radioactive ATP and the analysis of reaction products. This indicates that the paper focuses on the enzymatic activity of the purified proteins, which is a key characteristic of experimental enzymology.\n",
        "doc_id": "462f1ffb-11a9-44c1-aeaa-a07f24dff500"
      }
    ]
  },
  "26160102": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/26160102.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the NSUN6 protein, which is a methyltransferase, from Escherichia coli. The paper details in vitro methylation assays that measure the activity of the purified NSUN6 enzyme on specific tRNA substrates, indicating that NSUN6 is an active RNA methyltransferase. The methods include the use of recombinant NSUN6 in the presence of 3H-labeled S-adenosyl methionine to assess methylation activity, which is a clear indication of an enzymatic assay being performed.\n",
        "doc_id": "fbb0222e-fdcf-454d-8c02-5bd9ca5e128e"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation assays performed with recombinant NSUN6, which is a protein/enzyme, and details the experimental setup including the use of tritiated S-adenosyl-methionine as the methyl group donor. The paper describes the purification of the NSUN6 protein and its enzymatic activity on various tRNA substrates, which is a key characteristic of experimental enzymology. Additionally, it includes specific experimental results and methodologies related to the enzymatic assays, such as the use of denaturing PAGE and autoradiography to analyze the methylation of tRNA, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "d91e9caa-9228-4677-b352-641383ac9f12"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the methylation of tRNAs by the enzyme NSUN6, detailing in vitro methylation assays that were performed to confirm the target nucleotide for methylation. It mentions the use of synthetic tRNAs in these assays and provides results indicating the methylation status of various tRNA isoacceptors, which is a key aspect of experimental enzymology. The paper also describes the importance of specific nucleotide sequences for the enzyme's activity, which aligns with the typical focus of experimental enzymology on enzyme function and substrate specificity.\n",
        "doc_id": "696d63a2-dd61-4b37-a393-4644b7a9ed57"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the NSUN6 protein in E. coli, detailing the methods used for protein induction, lysis, and purification using NiNTA-Sepharose and amylose beads. Additionally, the paper describes the preparation of synthetic tRNAs and the use of in vitro transcription, which indicates that enzymatic assays may be performed to measure the activity of the purified enzyme. The mention of specific techniques such as Northern blotting and the use of radioactive labeling further supports the experimental enzymology focus of the paper.\n",
        "doc_id": "b63e1f5b-1f6d-442a-948c-b7537f6ac432"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the methylation of RNA substrates using recombinant NSUN6, which indicates the overexpression and purification of this enzyme. The paper details an in vitro methylation assay, including specific conditions for the reaction, the use of [³H]-SAM, and the methods for analyzing the results (e.g., separation on polyacrylamide gels and exposure to X-ray film). These elements are characteristic of experimental enzymology, as they focus on measuring the activity of a purified enzyme in a controlled environment.\n",
        "doc_id": "2e6235f4-ad74-4098-b08e-c84882ca32c3"
      }
    ]
  },
  "26001783": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/26001783.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the purification of the carnosine N-methyltransferase enzyme from rat muscles, detailing the purification process and the identification of the enzyme through mass spectrometry. The paper also describes the enzymatic activity of the purified enzyme, confirming its ability to catalyze the formation of anserine from carnosine, which is a key aspect of experimental enzymology. Additionally, it mentions the expression of the UPF0586 protein in COS-7 cells and the subsequent assays that demonstrate the enzyme's activity, which aligns with the typical structure and focus of experimental enzymology papers.\n",
        "doc_id": "c10f0592-61cc-4592-a72b-c2e617675120"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the carnosine N-methyltransferase enzyme, detailing the methods used for purification from rat leg muscles, including the use of various chromatography techniques (DEAE-Sepharose, Q-Sepharose, Superdex 200, and HiScreen Blue Sepharose). Additionally, it describes an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically by measuring the incorporation of a methyl group from S-[methyl-³H]adenosyl-L-methionine into carnosine. This combination of enzyme purification and activity measurement is characteristic of experimental enzymology studies.\n",
        "doc_id": "0b1a55fd-ce07-4322-868e-30b37678fd04"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of a protein (carnosine N-methyltransferase) and includes detailed methods for the purification process, such as using HisTrap HP columns and various buffers. Additionally, it mentions the use of enzymatic assays to measure the activity of the purified enzyme, specifically in the context of analyzing carnosine and anserine content, which indicates that the enzymatic activity of the protein is being assessed. The paper also describes the use of techniques like SDS-PAGE and Western blotting for expression analysis, which are common in experimental enzymology studies.\n",
        "doc_id": "a944218c-56c7-4d27-9368-b484f101b93f"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the UPF0586 protein from various sources (rat, human, chicken, and yeast) using affinity chromatography, as detailed in the Methods section. The paper also describes an in vitro enzymatic assay where the purified enzyme is incubated with substrates (carnosine and SAM) to measure the activity of the enzyme, which is indicated by the formation of a methylated dipeptide. The use of SDS-PAGE and Western blot analysis to confirm the purity and identity of the enzyme further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "935f38c9-6442-4844-8184-d3daa4267c1c"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and identification of rat carnosine N-methyltransferase, detailing the purification process involving chromatography techniques and the measurement of enzyme activity through the incorporation of a radiolabeled methyl group into carnosine. The paper also mentions the calculation of kinetic parameters (Vₘₐₓ, Kₘ, and kcat) for the methyltransferase activity, which are typical components of experimental enzymology studies. The methods section includes specific techniques for enzyme purification and activity assays, indicating a focus on the experimental aspects of enzymology.\n",
        "doc_id": "83ed64fd-5530-4c70-a223-2eca99533c6a"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of carnosine N-methyltransferase from rat skeletal muscles, including details on the purification process and the enzymatic activity of the recombinant enzyme. The paper describes the expression of the enzyme in COS-7 and HEK-293T cells, the use of a radiochemical assay to measure the synthesis of anserine, and the verification of the product identity through HPLC-HILIC MS/MS. Additionally, it presents data on the enzyme's activity under various conditions, which is typical of experimental enzymology studies.\n",
        "doc_id": "604ba624-d24e-481f-95a2-a185c55fd0a7"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification of the rat carnosine N-methyltransferase enzyme through various chromatography techniques, which is a key aspect of experimental enzymology. Additionally, it mentions the measurement of enzymatic activity using carnosine as a substrate, along with kinetic properties such as Kₘ and V₀ values, which are essential for understanding enzyme function. The paper also includes details about the methods used to analyze the enzyme's activity and the conditions under which these measurements were taken, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "b232b593-3b9c-47a7-903b-98684b79d62f"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the carnosine N-methyltransferase enzyme (UPF0586) in COS-7 cells, as well as the investigation of its enzymatic activity related to anserine production. The paper mentions the transfection of cells with plasmids to express the enzyme and the subsequent measurement of carnosine and anserine concentrations using HPLC-HILIC, which indicates an in vitro enzymatic assay to assess the activity of the purified enzyme. This aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "55028831-3ffb-456d-8ac3-10bea0a6394f"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the UPF0586 protein from various sources (yeast, chicken, rat, and human) and describes an in vitro enzymatic assay where cell-free lysates are incubated with carnosine and [³H]SAM to measure the production of anserine. The methods section includes details about the experimental setup, such as the use of Western blot analysis to verify the presence of the recombinant protein and the chromatographic separation of the reaction products, which are key components of experimental enzymology studies.\n",
        "doc_id": "294eb3cd-a8ee-42f1-b0e5-bb522a5c69b7"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the UPF0586 protein, which is identified as carnosine N-methyltransferase. The paper details the enzymatic activity of this protein, including the transfer of a methyl group from SAM to carnosine, yielding anserine. The methods section mentions incubating the enzyme with substrates and analyzing the products using mass spectrometry, which are key components of an in vitro enzymatic assay. Additionally, the paper provides data on the enzyme's activity under varying conditions, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "0bd3f315-c6d4-44bd-b5ef-cecfff7819e7"
      },
      {
        "page": 13,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of UPF0586 proteins from various species, including rat, human, chicken, and yeast, and details the in vitro enzymatic assays used to measure the activity of these purified enzymes. Specifically, it describes the methylation reactions catalyzed by these proteins, including the use of S-adenosyl-L-methionine (SAM) as a methyl group donor and various L-histidine-containing peptides as acceptors. The paper also provides kinetic properties of the enzymes, such as Vmax and Km values, which are essential components of enzymatic assays. This focus on enzyme activity and characterization aligns well with the criteria for experimental enzymology.\n",
        "doc_id": "5e723b62-d678-4f62-9076-27ddde24535b"
      },
      {
        "page": 14,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the carnosine N-methyltransferase enzyme (UPF0586) in COS-7 cells, as indicated by the mention of transfection with plasmids encoding the enzyme and the subsequent analysis of the enzyme's activity in relation to carnosine and anserine production. The paper also includes details about the experimental procedures, such as the use of Western blot analysis to confirm the overexpression of the recombinant proteins, which is a common method in experimental enzymology to assess the presence and quantity of the enzyme being studied. Additionally, the paper implies the measurement of enzymatic activity through the accumulation of products (carnosine and anserine) in the cell culture medium, which aligns with the typical focus of experimental enzymology on in vitro enzymatic assays.\n",
        "doc_id": "0b2348f4-b346-4cc2-8879-e7e8152bf7b9"
      }
    ]
  },
  "12917423": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/12917423.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the cloning, expression, and purification of the SARS coronavirus NTPase/helicase protein, which is a key aspect of experimental enzymology. The paper details the characterization of the enzyme's helicase and NTPase activities, including specific assays to measure these activities, such as the high throughput phosphate release assay. The quantitative analysis of the enzyme's interaction with various nucleotides and the description of its enzymatic properties further confirm that this paper fits the criteria for an experimental enzymology study.\n",
        "doc_id": "1feccfd7-c28c-43f8-b2f6-b0f0e2a59def"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification and characterization of the SARS NTPase/helicase, detailing the overexpression of the protein in a bacterial system, the purification process using nickel affinity chromatography, and the subsequent enzymatic assays to measure the enzyme's activity. Specifically, it describes NTPase assays that measure phosphate release, which is a clear indication of enzymatic activity, and includes methods for preparing DNA substrates and conducting unwinding assays, all of which are characteristic of experimental enzymology studies.\n",
        "doc_id": "88685b69-a6cc-424b-97b8-e99f2e9ee220"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of the SARS coronavirus NTPase/helicase, including the overexpression and purification of the His-tagged protein using nickel affinity chromatography. The paper also details in vitro enzymatic assays to measure the activity of the purified enzyme, specifically the hydrolysis of NTPs and the ATPase activity, which are quantified using a colorimetric assay. The results are analyzed using Michaelis-Menten kinetics, indicating a clear focus on enzymatic activity and characterization, which are hallmarks of experimental enzymology.\n",
        "doc_id": "158c9cee-819e-49c9-be22-c7d220303b2b"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the expression, purification, and biochemical characterization of the SARS-CoV NTPase/helicase protein, which indicates that the authors have overexpressed and purified the enzyme. The paper also details the enzymatic assays performed to measure the enzyme's activity, such as the ATPase activity and the binding of polynucleotides, which are key components of experimental enzymology. The use of Michaelis-Menten kinetics to analyze the enzyme's activity further supports this classification, as it involves measuring the rate of reaction in relation to substrate concentration, a common practice in enzymology studies.\n",
        "doc_id": "0671ca7c-cdac-458b-8529-015b17c24ce0"
      }
    ]
  },
  "19929881": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/19929881.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the characterization of the Dim1B protein as a functional rRNA dimethyltransferase, including the complementation assays performed in E. coli to demonstrate its methyltransferase activity. The paper details the methods used to assess the enzyme's activity, such as the introduction of the Dim1B gene into a KsgA-deficient E. coli strain and the subsequent observation of N6-adenine methyltransferase activity. This indicates that the authors conducted in vitro enzymatic assays to measure the activity of the purified enzyme, which is a hallmark of experimental enzymology.\n",
        "doc_id": "1b620571-6f9e-4181-b472-a205fad6f11b"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of recombinant proteins Dim1A and Dim1B in Escherichia coli, which is a key aspect of experimental enzymology. The paper also describes in vitro transcription assays, indicating that enzymatic activity is being measured. Specifically, it mentions the use of recombinant proteins in transcription reactions, which aligns with the typical methodologies found in experimental enzymology studies.\n",
        "doc_id": "5f3b1dc3-ae76-4ffb-ad38-4a8fbb77997b"
      }
    ]
  },
  "22829772": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/22829772.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of a recombinant GST-tagged version of the C. elegans HEN1 homolog (C02F5.6) and tests this protein for its methylating activity on the 39 end of ssRNA molecules in vitro. The paper provides details about the enzymatic assay, including the effects of a 29O-methyl group on the substrate and the results of the methylation activity, which are key components of experimental enzymology.\n",
        "doc_id": "a5294a87-f9af-4bf4-8f3a-2f9f95c71add"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the GST-HENN-1 protein, as indicated by the mention of \"purified GST, GST-HENN-1 and GST-HENN-1(D151N) proteins used to perform methyltransferase assays.\" Additionally, it describes an in vitro methyltransferase activity assay where RNA oligos were incubated with the proteins and a labeled cofactor (14C-labelled SAM), which is a clear indication of measuring enzymatic activity. The paper also includes results from these assays, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "610eea38-4b46-4623-ac64-a671b596b129"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. The Methods section describes the overexpression and purification of the HENN-1 protein using GST beads, and it details an in vitro methyltransferase activity assay to measure the enzymatic activity of the purified HENN-1 protein. The assay includes specific conditions and reagents used, such as the reaction components and the method for analyzing the results, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "1645d8f4-1646-4332-92dc-f2c689bd0cc7"
      }
    ]
  },
  "23074192": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/23074192.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the protein Pmt1, which is a methyltransferase, and details the methods used for its purification, including the use of His6-tagging and affinity chromatography. Additionally, the paper describes in vitro enzymatic assays to measure the methylation activity of Pmt1 on tRNA substrates, indicating that the authors conducted experiments to assess the enzyme's activity under specific conditions. This aligns well with the characteristics of experimental enzymology papers, which focus on the functional analysis of enzymes through purification and activity assays.\n",
        "doc_id": "6b71ed8e-afad-48d8-a77a-77ae61c89fc3"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme Pmt1 from *S. pombe*, and it describes an in vitro tRNA methylation assay to measure the activity of the purified enzyme. The methods section details the incubation of total RNA or in vitro transcribed tRNA with the enzyme, the conditions of the reaction, and the subsequent analysis of the methylation activity, which are all key components of experimental enzymology. Additionally, the paper provides results that demonstrate the enzymatic activity of Pmt1, including the effects of specific mutations on its activity, which further supports its classification as an experimental enzymology study.\n",
        "doc_id": "74c16009-4c20-4c8d-9b5c-78db8d22d9a8"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the enzyme Pmt1 and its homologs, detailing the methods used to measure this activity through methylation assays with in vitro-transcribed tRNA. The paper describes the use of 3H-labeled AdoMet and the analysis of the results through urea-PAGE and autoradiography, which are typical methods in experimental enzymology to assess enzyme activity. Additionally, it mentions the purification of recombinant Dnmt2 homologs and the effects of specific mutations on enzyme activity, further indicating a focus on enzymatic assays and protein characterization.\n",
        "doc_id": "58b19e08-56d9-4edd-92ad-4f708817261d"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation of tRNA by the recombinant enzyme Pmt1, which is a clear indication of an enzymatic assay being performed. The paper details the overexpression of the Pmt1 enzyme and its purification, as well as the measurement of its activity through the incorporation of methyl groups into RNA substrates. The methods section mentions the use of recombinant Pmt1 in an in vitro methylation experiment, which aligns with the characteristics of experimental enzymology papers.\n",
        "doc_id": "8cdef5ea-29b8-48e8-b0c3-14e40ea2b24c"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation assays performed with recombinant Pmt1 and total RNA from cells grown under different media conditions, which directly measures the enzymatic activity of the purified enzyme. The paper details how the media composition affects the tRNA methylation activity of Pmt1, indicating that the authors conducted experiments to assess the enzyme's function in vitro. Additionally, the mention of recombinant Pmt1 and the analysis of its activity in various conditions aligns with the characteristics of experimental enzymology papers.\n",
        "doc_id": "0ca902c5-4086-4e75-9382-376f793299fb"
      }
    ]
  },
  "18162595": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/18162595.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the biochemical analysis of IAMT (Indole-3-acetic acid methyltransferase) from rice, which indicates that the authors likely performed enzymatic assays to measure the activity of the enzyme. The paper also mentions the determination of the three-dimensional structure of Arabidopsis IAMT and its comparison to other members of the SABATH family, which suggests that the authors engaged in protein purification and characterization, common practices in experimental enzymology. Additionally, the focus on substrate specificity and the structural analysis of the enzyme further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "6487e7cd-da15-42b8-8f68-8d9935e90461"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the OsIAMT1 protein, which is derived from the OsSABATH4 gene, and details the enzymatic assays performed to measure its activity with various substrates, including IAA. The paper provides specific activity measurements, optimal pH conditions, and kinetic parameters (Km and kcat values) for the enzyme, which are all key components of experimental enzymology. Additionally, it describes the methods used to analyze the product of the enzymatic reaction, confirming the enzyme's function.\n",
        "doc_id": "0a701d83-1caa-4967-8d1b-de7cb72650ca"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of the OstIAMT1 protein, as indicated by the mention of \"recombinant OstIAMT1 protein\" and the \"enzyme assay catalyzed by recombinant OstIAMT1 protein with IAA as the substrate.\" Additionally, the paper includes details about a GC-MS analysis of the product of the enzyme assay, which is a common method used to measure the activity of purified enzymes. This focus on enzymatic assays and the characterization of enzyme activity aligns well with the criteria for experimental enzymology papers.\n",
        "doc_id": "21291e86-ce44-41ca-b878-b54fd6c2b8c1"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme OsIAMT1, detailing the methods used for protein expression in E. coli, purification using nickel nitrilotriacetic acid agarose, and verification of protein purity by SDS-PAGE. Furthermore, it includes an in vitro enzymatic assay (radiochemical MT activity assay) to measure the activity of the purified enzyme, where the reaction conditions, substrates, and methods for quantifying the reaction products are clearly described. The paper also discusses kinetic parameters and substrate specificity, which are key aspects of experimental enzymology.\n",
        "doc_id": "0be970b6-e32c-477d-9e72-8df3ab0bcdfa"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme OsIAMT1, and it describes in detail the methods used to perform enzymatic assays to measure the activity of this purified enzyme. Specifically, it mentions the incubation of purified OsIAMT1 with substrates and the subsequent analysis of the reaction products using GC-MS, which is a clear indication of an in vitro enzymatic assay. The paper also includes controls to validate the enzymatic activity, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "7908583d-20c1-44db-92b0-c57c0bb97cea"
      }
    ]
  },
  "19439410": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/19439410.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the inhibition of mycolic acid methyltransferases (MA-MTs) from Mycobacterium tuberculosis and Mycobacterium smegmatis, specifically mentioning the use of structural analogs of the AdoMet cofactor to inhibit these enzymes. The paper describes in vitro assays to measure the inhibitory effects of the bisubstrate inhibitor S-adenosyl-N-decyl-aminoethyl on the activity of MA-MTs, providing IC₅₀ values, which is a key aspect of experimental enzymology. Additionally, the investigation of the interaction between the enzyme and the inhibitor through x-ray crystallography further supports its classification as an experimental enzymology paper, as it involves the study of enzyme activity and structure.\n",
        "doc_id": "2e853307-ff59-467f-8e68-a604f843eeb7"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the inhibition of mycolic acid methyltransferases (MA-MTs) and includes details about the overexpression and purification of the enzyme Hma (MmaA4) from Mycobacterium tuberculosis, as well as the investigation of its interactions with various inhibitors like SADAE and AdoHcy. The Methods section mentions the growth of specific strains of Mycobacterium and the preparation of recombinant strains, which indicates that the authors are working with purified enzymes and conducting in vitro assays to measure enzyme activity and inhibition. This aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "3e04a577-cd26-4fe0-b927-a5908e737316"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the evaluation of the ability of AdoMet analogs to inhibit mycolic acid biosynthesis in vitro, which involves a detailed description of the in vitro enzymatic assay setup, including the reaction medium composition, incubation conditions, and methods for analyzing the products (e.g., TLC and phosphorimaging). The paper also mentions the purification of cell wall extracts and the measurement of enzyme activity, which are key components of experimental enzymology.\n",
        "doc_id": "1718baef-c110-4068-b9c8-6c01f2ed634b"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro enzymatic assays to measure the activity of mycolic acid methyltransferases (MA-MT) using cell wall extracts from *M. smegmatis*. The paper details the effects of various inhibitors on MA-MT activities, indicating that the authors performed assays to assess the enzymatic activity in the presence of different compounds. Additionally, it mentions the use of radiolabeled substrates and techniques like TLC and phosphorimaging to analyze the results, which are common practices in experimental enzymology. The focus on enzyme activity and the methods used to measure it clearly align with the characteristics of an experimental enzymology paper.\n",
        "doc_id": "e1e436a2-73b6-451a-8307-406552519efd"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the inhibition of mycolic acid methyltransferases (MA-MTs) and mentions the evaluation of the ability of certain molecules to inhibit these enzymes in vitro. It specifically states that the effects of SADAE on MA-MT activities were demonstrated in vitro, using both wild-type and recombinant strains, and describes the absence of neosynthesis of various mycolic acids following treatment with SADAE. This indicates that there were enzymatic assays performed to measure the activity of the enzymes, which is a key characteristic of experimental enzymology papers. Additionally, the paper discusses the structural interactions between the inhibitor and the enzyme, further supporting its focus on enzymatic activity and inhibition.\n",
        "doc_id": "4f9d27c3-5574-4978-b39e-b2d5739296dc"
      }
    ]
  },
  "6508744": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/6508744.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme spermidine synthase, detailing the methods used to isolate the enzyme from bacterial cells, including centrifugation and dialysis. The paper also describes an in vitro enzymatic assay to measure the activity of the purified enzyme by assessing the production of [14C]methylthioadenosine from decarboxylated S-adenosyl-L-[Me-14C]methionine, which is a clear indication of enzymatic activity. Additionally, the paper includes specific details about the conditions under which the enzymatic assays were performed, such as temperature and pH, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "45f617d7-21b6-4c30-bed4-14d59b0bd19f"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the activity of bacterial spermidine synthase and includes details about measuring the enzyme's activity in the presence of dicyclohexylamine, which is indicative of an in vitro enzymatic assay. The text mentions that the \"spermidine synthase activity from Strep. uberis\" was measured and that results were expressed as percentages of activity in the absence of any inhibitor, which aligns with the typical structure of experimental enzymology papers that focus on enzyme activity assays.\n",
        "doc_id": "c95dad2a-9ebc-44da-840c-9fb44882232a"
      }
    ]
  },
  "30054361": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/30054361.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the heterologous expression of a halogenase enzyme in Escherichia coli, followed by an in vitro enzymatic assay where the potential enzymatic product, OTA, is detected using HPLC with fluorescence detection. The paper details the transformation of OTB to OTA through halogenation, indicating a clear focus on enzyme activity and the biochemical processes involved in OTA biosynthesis. Additionally, it mentions the effects of gene inactivation on OTA production, further emphasizing the enzymatic functions being studied.\n",
        "doc_id": "2c75d184-06c8-46b1-a041-01732d67e101"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of a halogenase enzyme in E. coli, as indicated by the mention of \"Expression of halogenase in E. coli BL21\" and the use of \"HPLC-FLD analysis of the enzyme activity.\" The paper includes details about the recombinant vector used for expression and the enzymatic assays performed to measure the activity of the halogenase with specific substrates (OTB and OTb), which are key components of experimental enzymology.\n",
        "doc_id": "4e503fb0-6385-4d23-8d35-549a1b2ca317"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of a halogenase gene in E. coli, detailing the methods used for protein production, including optimization of induction conditions and subsequent analysis of the expressed protein. The paper also describes functional analysis of the expressed halogenase, indicating that enzymatic assays were performed to measure the activity of the enzyme in relation to OTA and related metabolites. This focus on protein expression, purification, and functional assays aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "0b610035-299a-4e8f-bd95-d9297a306ad2"
      }
    ]
  },
  "30934718": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/30934718.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the cloning, expression, and purification of a protein (COMT-S) from P. praeruptorum, which is identified as a caffeic acid 3-O-methyltransferase. The paper details the determination of enzymatic activity with various coumarins, indicating that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. This aligns with the typical characteristics of experimental enzymology papers, which focus on the overexpression and purification of enzymes followed by assays to evaluate their activity.\n",
        "doc_id": "ce646b96-5c54-4e2e-bc7a-d53418510a68"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the functional characterization of the enzyme COMT-S, including the enzymatic reaction products generated by recombinant COMT-S and the substrates it can accept. The paper details the effects of pH and metal ions on the catalytic activity of COMT-S, which indicates that in vitro enzymatic assays were performed to measure the enzyme's activity. Additionally, the mention of expression profiles and treatments affecting the enzyme further supports the experimental enzymology focus of the study.\n",
        "doc_id": "d69d76fd-24c9-4acb-b142-1afb56191a6f"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the COMT-S protein, as indicated by the mention of crystallization, SDS-PAGE, and elution volume analysis of the purified protein. Additionally, it includes an in vitro enzymatic assay to measure the activity of the purified enzyme, as evidenced by the description of the activity of wild type COMT-S and its mutants toward esculetin, along with the calculation of yields for the products isoscopoletin and scopoletin. The mention of the methods for analysis and reaction process further supports that this paper is focused on experimental enzymology.\n",
        "doc_id": "9ea2f845-d16d-4723-b284-668d062a0aae"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the COMT-S protein from P. praeruptorum, detailing the use of an expression vector (pET28a) and a purification method involving a 6× His tag and gel-filtration chromatography. This indicates that the authors are engaged in the experimental aspects of enzymology, specifically in the purification of an enzyme. The mention of protein expression and purification methods aligns with the typical structure of experimental enzymology papers, which often include in vitro assays to measure enzyme activity, although the specific enzymatic assays are not detailed in the provided text.\n",
        "doc_id": "93e9eb0b-3c9b-439e-a9e7-a128cb6ccd97"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins (COMT-S and PpBMT) and includes a detailed description of enzymatic activity assays performed to measure the activity of the purified enzymes. The methods section outlines the conditions under which the enzymatic assays were conducted, including the use of specific substrates (coumarins and SAM), buffer conditions, and variations in pH and ion concentrations. Additionally, it mentions the use of PCR for generating mutations and the transformation of E. coli for protein expression, which are common practices in experimental enzymology.\n",
        "doc_id": "23a343fb-4b8b-49fa-ab0f-2e2287a2fbb4"
      }
    ]
  },
  "32437639": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/32437639.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The text discusses the overexpression and purification of the Dnmt5 protein from the yeast Cryptococcus neoformans, which is a key aspect of experimental enzymology. It details the biochemical characterization of the enzyme, including its activity in vitro, specifically mentioning the conditions under which the enzyme's DNA methyltransferase activity was tested, such as the requirement for ATP and the use of various DNA substrates. The paper also describes the methods used to assess the enzyme's specificity and activity, which are typical components of experimental enzymology studies.\n",
        "doc_id": "c51eeb87-be61-4077-b219-10779754a52f"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of Dnmt5, an ATP-dependent DNA methyltransferase, and includes details about the experimental setup such as the use of various DNA substrates (unmethylated, hemimethylated, and symmetrically methylated) and the measurement of the enzyme's activity in the presence or absence of ATP. The paper provides specific data on the kinetics of DNA methylation, average initial rates of DNMT activity, and the conditions under which these measurements were taken, which are all indicative of an in vitro enzymatic assay.\n",
        "doc_id": "973c7b15-27c0-475b-a06b-c2189d4e39d8"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Dnmt5 enzyme, as well as the in vitro enzymatic assays used to measure its activity on various DNA substrates. The paper details the ATPase activity of Dnmt5, the conditions required for its activity, and the effects of different DNA methylation states on its enzymatic function. Specifically, it describes how the enzyme's activity is influenced by the presence of ATP and the methylation state of the DNA, which are key components of experimental enzymology. The methods section includes descriptions of assays that measure the enzyme's activity, confirming its classification as an experimental enzymology paper.\n",
        "doc_id": "3ada1fb0-e6c3-41e5-8fa5-a5af7886cf09"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of a truncated form of the Dnmt5 protein and assesses its ability to bind DNA using an electrophoretic mobility shift assay (EMSA), which is a common method in enzymology to measure enzyme activity. The paper also details the effects of nucleotides on the DNA-binding ability of Dnmt5, indicating a coupling between its SNF2 and DNMT domains, and includes quantitative EMSA experiments to validate these effects. Additionally, it explores the ATPase activity of Dnmt5 in relation to DNA features, which further emphasizes the enzymatic assays being performed. Overall, the focus on protein purification, binding assays, and enzymatic activity aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "dfb48a86-cd3e-4e6c-b6e6-e497060269da"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the ATPase activity of the Dnmt5 enzyme in the presence of various DNA substrates, which indicates that the authors are measuring the enzymatic activity of a purified enzyme. The paper includes details about the experimental setup, such as the concentrations of Dnmt5 and the DNA substrates used, as well as the methodology for assessing ATPase activity. The mention of average rates of ATPase activity and the normalization of these rates to a control further supports that this is an experimental enzymology study focused on enzyme kinetics and activity assays.\n",
        "doc_id": "43d634f1-008a-465a-9ce0-588e0e3311dd"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the biochemical characterization of the Dnmt5 enzyme, including its ATPase and methyltransferase activities. It mentions the use of in vitro assays to measure the enzyme's activity, specifically noting the measurement of kcat and KMapp,DNA for various DNA substrates using an ATPase assay. Additionally, the paper describes the generation of specific DNA substrates and their interaction with Dnmt5, which is a key aspect of experimental enzymology involving the overexpression and purification of enzymes followed by activity assays.\n",
        "doc_id": "a5a0d8d8-5dc0-4c4e-b853-c4875ea36c79"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Dnmt5 protein, as well as the performance of various enzymatic assays, including methyltransferase and ATPase assays. The methods section explicitly mentions the expression and purification of recombinant proteins, which is a key aspect of experimental enzymology. Additionally, the paper explores the enzymatic activity of Dnmt5 in relation to ATP hydrolysis and substrate specificity, indicating a focus on the functional analysis of the enzyme.\n",
        "doc_id": "a08fc657-19f7-4291-9ffd-829064572163"
      },
      {
        "page": 16,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Dnmt5 protein from various host organisms, including E. coli and S. cerevisiae, which is detailed in the Methods section. Additionally, it describes an in vitro enzymatic assay, specifically a DNA methyltransferase assay, to measure the activity of the purified enzyme. The paper outlines the conditions under which the enzymatic reactions were performed, including the use of specific substrates and the detection of methylation activity, which are key components of experimental enzymology.\n",
        "doc_id": "ed9db801-7413-4220-a97c-2faa7a33f691"
      },
      {
        "page": 17,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Dnmt5 enzyme, as well as the use of an ATPase assay to measure the enzyme's activity. The methods section describes the preparation of the enzyme, the conditions for the ATPase activity assay, and the monitoring of the reaction using a plate reader, which are all key components of experimental enzymology. Additionally, the paper includes details about the experimental setup, such as the concentrations of substrates and the conditions under which the assays were performed, which further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "da59f314-3cb0-4ff8-8f45-7568079807c0"
      }
    ]
  },
  "17301146": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/17301146.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the dengue virus RNA-dependent RNA polymerase (RdRp) catalytic domain, and it mentions a high-throughput in vitro assay that recapitulates the enzymatic activity of this polymerase. The paper provides details about the structure of the enzyme and its functional domains, which are essential for understanding its enzymatic activity. The focus on the enzymatic assay and the characterization of the enzyme's structure indicates that this paper fits well within the realm of experimental enzymology.\n",
        "doc_id": "e7064ec9-7cc0-4e4e-8221-c7c7907f8e27"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the DENV NS5 protein and its truncated constructs, as well as the in vitro enzymatic assays used to measure the activity of the purified enzyme. Specifically, it details a polymerase assay format that incorporates radioactive GTP and describes the conditions for steady-state kinetics of RNA synthesis by the DENV 3 RdRp, including the concentrations of enzyme and substrates used. The paper also mentions kinetic analysis and the determination of IC₅₀ values, which are typical components of experimental enzymology studies.\n",
        "doc_id": "26415372-1ef0-4b3e-b4c3-f6bb9d685104"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the DENV 3 RdRp enzyme, detailing the cloning, expression, and purification processes in the Methods section. Additionally, it describes an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically mentioning the conditions under which the NS5 RdRp activity was measured, including the use of a scintillation proximity assay (SPA) to assess the enzyme's activity and the determination of the inhibitory concentration of a nucleoside analog. These elements clearly indicate that the paper focuses on experimental enzymology.\n",
        "doc_id": "16fe2f64-27fd-4ad9-9b5b-5481faf11c47"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the DENV 3 RdRp enzyme, detailing the methods used to express the protein in high quantity and purify it to 95% purity. Additionally, the paper describes an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically mentioning the setup of a scintillation proximity assay (SPA) to determine the activity of the recombinant protein and its inhibition by 3*dGTP. This focus on both the purification of the enzyme and the measurement of its enzymatic activity aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "28cb10da-f70d-44b6-86ce-e04ce79cb825"
      }
    ]
  },
  "16571831": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/16571831.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a protein/enzyme, specifically the chymotrypsin-like proteinase (Mpro) from equine torovirus (EToV). The methods section details the cloning of the Mpro coding region into expression vectors, the induction of protein expression in E. coli, and the purification of the His-tagged protein using Ni-nitrilotriacetic acid affinity chromatography. Additionally, the paper mentions the biochemical characterization of the enzyme, which implies that enzymatic assays to measure the activity of the purified enzyme may be included, aligning with the typical focus of experimental enzymology papers.\n",
        "doc_id": "72db698a-6344-4563-8c13-e85a29035cbe"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the torovirus Mpro protein in E. coli, detailing the use of IPTG to induce expression and the analysis of the resulting protein products through SDS-PAGE. The paper also describes the characterization of the proteolytic activity of the Mpro enzyme, including the identification of cleavage products and the use of Edman degradation for sequencing, which are key components of enzymatic assays. The focus on the functional analysis of the enzyme and its activity further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "562f5b16-294f-4815-9f84-d6c7fb5861e6"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of the EToV Mᵖʳᵒ protein, including details about the constructs used for expression in E. coli and the analysis of the resulting protein products. The paper also describes mutagenesis of predicted active-site residues and assesses their effects on the proteolytic activity of the mutant proteinases, indicating that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. The mention of analyzing processing activities and the effects of specific amino acid substitutions on enzymatic function further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "f1e5d9b1-4ca4-4d21-a0c3-ba8ac77831f8"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the biochemical characterization of the torovirus main proteinase (Mᵖʳᵒ), including the design of a trans-cleavage assay to assess the enzymatic activity of the proteinase. The paper mentions the overexpression and purification of the Mᵖʳᵒ enzyme and its substrate, as well as the effects of specific amino acid substitutions on the enzyme's activity, which are key components of experimental enzymology. The use of assays to measure the activity of the purified enzyme and the detailed examination of its cleavage specificity further support its classification as an experimental enzymology paper.\n",
        "doc_id": "9466b3d9-4202-499c-bebb-dd812ddb91c5"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the EToV Mᵖʳᵒ proteinase, as well as the characterization of its catalytic residues and substrate specificity. The paper mentions enzymatic assays, specifically a trans-cleavage assay that tests the processing efficacy of Mᵖʳᵒ on an artificial substrate, which is a key component of experimental enzymology. Additionally, the paper explores the effects of site-directed mutagenesis on enzymatic activity, further indicating a focus on enzyme function and activity measurement.\n",
        "doc_id": "f54ce86e-47bb-4705-9753-09a5418a9831"
      }
    ]
  },
  "20854656": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/20854656.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. The study discusses the recombinant purification of the Rv1694 protein from Mycobacterium tuberculosis and demonstrates its enzymatic activity, specifically its ribosomal RNA methylation activity. The paper details the in vitro assays that confirm the hemolytic activity of the purified protein and its ability to incorporate methyl groups from [3H]-S-adenosylmethionine into isolated ribosomes, which is a clear indication of enzymatic function. The methods used to characterize the protein's activity and the results obtained from these assays align well with the criteria for experimental enzymology.\n",
        "doc_id": "370e360b-d4f3-460f-b0a3-1ecb29c27971"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the characterization of the Rv1694 protein, which is suggested to have both hemolytic and RNA methyltransferase activities. It mentions the need for detailed characterization of Rv1694 as purified protein to exhibit these activities under in vitro conditions. This indicates that the authors are likely to perform enzymatic assays to measure the activity of the purified enzyme, which is a key aspect of experimental enzymology. Additionally, the paper references experimental evidence supporting the activities of Rv1694, further aligning it with the characteristics of an experimental enzymology study.\n",
        "doc_id": "4a692954-925c-4e08-b6bb-4d6a6244656a"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the cloning, expression, and purification of the Rv1694 protein, which is identified as a ribosomal RNA methyltransferase. The methods section mentions the use of E. coli for overexpression and the purification process using Ni-NTA affinity columns, indicating a focus on protein/enzyme handling. Additionally, the paper describes the characterization of the purified protein, including its structural analysis through Circular Dichroism (CD) and mass spectrometry, which are common practices in experimental enzymology to confirm the integrity and functionality of the enzyme. The mention of the enzyme's homology with other methyltransferases further supports its enzymatic role.\n",
        "doc_id": "ee18f463-4a36-4295-abc1-9f11359fa0d4"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the cloning, expression, and purification of the Rv1694 protein in E. coli, which is a key aspect of experimental enzymology. It mentions the use of a 6-histidine tag for purification via Ni-NTA affinity chromatography, and the purification process is confirmed by SDS-PAGE analysis. Additionally, the paper describes an in vitro assay to measure the hemolytic activity of the purified Rv1694, providing specific details about the conditions and results of the assay, which is a hallmark of experimental enzymology studies.\n",
        "doc_id": "e0d72490-07f8-4047-aafa-eae71813e022"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of the Rv1694 protein, including its hemolytic activity, which is a measure of enzymatic function. The paper describes the generation of Rv1694 through in vitro transcription and translation (IVTT) and details the hemolytic assays performed to assess the activity of the purified enzyme, including the measurement of absorbance to quantify hemolysis. The results indicate the dependence of hemolytic activity on specific conditions, such as the presence of reducing agents, which is a typical focus in experimental enzymology studies.\n",
        "doc_id": "6518ce04-fc2c-4633-aa30-2949f9fd371b"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the ribosomal RNA methylase activity of the Rv1694 protein, which indicates that the authors are investigating the enzymatic function of this protein. The paper mentions attempts to evaluate the methyltransferase activity of Rv1694, including monitoring growth rates of E. coli transformed with Rv1694 and analyzing in vitro translation using S30 extracts. These details suggest that the authors are conducting enzymatic assays to measure the activity of the purified enzyme, which is a key characteristic of experimental enzymology papers.\n",
        "doc_id": "03f5e4bb-aea2-46f8-9e15-adb58f5ea57b"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the purified Rv1694 protein on ribosomes, which involves measuring the enzymatic activity of Rv1694 in transferring a methyl group from S-adenosylmethionine to ribosomal RNA. The paper describes the experimental setup, including the use of purified Rv1694 and the conditions under which the methylation reaction was assessed, indicating that it includes an enzymatic assay to measure the activity of the enzyme. Additionally, the paper mentions the purification of Rv1694 and its role as a ribosomal RNA methylase, which are key components of experimental enzymology.\n",
        "doc_id": "0fbe7058-966c-4049-a2cb-d43a766f1728"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the purification and characterization of the Rv1694 protein, which is associated with ribosomal RNA methylation activity and exhibits hemolytic properties. It mentions the assessment of the enzyme's activity under in vitro conditions, specifically highlighting the hemolytic activity of the purified protein and its sensitivity to reducing agents. The paper also describes the oligomerization of Rv1694 on cell membranes and its role in destabilizing membranes, which are key aspects of experimental enzymology. The presence of detailed experimental results, such as those shown in figures and the discussion of enzymatic activity, further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "45d6f1c0-ea94-496e-9989-4b6c5394d0a6"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The text describes the cloning, expression, and purification of the Rv1694 protein, which is a key aspect of experimental enzymology. It details the methods used to purify the protein using a Ni-NTA column and confirms the purity of the eluted protein through SDS-PAGE. Additionally, the paper discusses the enzymatic activity of Rv1694, specifically its role in contact-dependent hemolysis, which indicates that the authors are measuring the activity of the purified enzyme in vitro. This aligns with the typical structure and content of experimental enzymology papers, which focus on the characterization and activity measurement of enzymes.\n",
        "doc_id": "7296a26a-ad28-4707-b795-f2946aa03084"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the Rv1694 protein and includes detailed methods for conducting enzymatic assays, such as hemolysis assays and RBC membrane binding assays. The paper describes the preparation of purified Rv1694 and its interaction with red blood cells, measuring the absorbance to assess enzyme activity. Additionally, it mentions the use of specific buffers and conditions for these assays, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "3e0abfb2-a9ca-41d2-ab4e-d80ece58dc2e"
      },
      {
        "page": 13,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the preparation of S30 extracts from recombinant E. coli expressing a specific protein (Rv1694) and details the in vitro translation activity measurements, which involve enzymatic assays to quantify translation efficiency. The methods section describes the purification of ribosomes and the methylation assay, indicating that the authors are measuring the activity of the purified components, which is a hallmark of experimental enzymology.\n",
        "doc_id": "e000f7f8-51f8-4e3f-b5b2-60f7ee36feec"
      }
    ]
  },
  "30765518": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/30765518.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro translation inhibition of luciferase mRNA, which is measured by the percent decrease in luminescence in the presence of FMRP and other inhibitors. The paper describes the use of a rabbit reticulocyte lysate for the translation assay, indicating that the authors performed an enzymatic assay to measure the activity of the purified enzyme (in this case, the translation process). Additionally, the paper mentions the correlation between translation inhibition and turbidity, which further supports the experimental enzymology focus. Overall, the presence of an in vitro enzymatic assay and the detailed discussion of translation inhibition point to this being an experimental enzymology paper.\n",
        "doc_id": "18bc8b9a-97ef-4594-b94a-52040f1ec998"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins, specifically FMRP and its variants, in Escherichia coli, which is a common method in experimental enzymology. Additionally, it mentions in vitro assays, such as the in vitro translation of luciferase mRNA and the use of a luciferase assay to monitor the activity of the translation, which aligns with the typical methodologies used in experimental enzymology to measure enzyme activity. The paper also includes details about protein modifications (phosphorylation and methylation) and binding assays, which are relevant to understanding enzyme function and regulation.\n",
        "doc_id": "1db77740-db09-4dcc-8573-219f742e089f"
      }
    ]
  },
  "19103757": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/19103757.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro translation inhibition of luciferase mRNA, which is measured by the percent decrease in luminescence in the presence of FMRP and other inhibitors. The paper describes the use of a rabbit reticulocyte lysate for the translation assay, indicating that the authors performed an enzymatic assay to measure the activity of the purified enzyme (in this case, the translation process). Additionally, the paper mentions the correlation between translation inhibition and turbidity, which further supports the experimental enzymology focus. Overall, the presence of an in vitro enzymatic assay and the detailed discussion of translation inhibition point to this being an experimental enzymology paper.\n",
        "doc_id": "7924907b-7738-4c9d-abb1-b896321a3267"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins, specifically FMRP and its variants, in Escherichia coli, which is a common method in experimental enzymology. Additionally, it mentions in vitro assays, such as the in vitro translation of luciferase mRNA and the use of a luciferase assay to monitor the activity of the translation, which aligns with the typical methodologies used in experimental enzymology to measure enzyme activity. The paper also includes details about protein modifications (phosphorylation and methylation) and binding assays, which are relevant to understanding enzyme function and regulation.\n",
        "doc_id": "daf5c762-218b-4f02-a07f-033144ad4bd4"
      }
    ]
  },
  "28441781": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28441781.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the guanylyltransferase and methyltransferase activities of the NS5 protein, detailing the mechanisms of these enzymatic reactions, including the involvement of specific substrates (like GTP and S-adenosylmethionine) and the roles of certain amino acids in catalysis. The paper describes in vitro experiments and the interactions between the NS5 and NS3 proteins, which are indicative of enzymatic assays and the study of enzyme activity. The focus on the enzymatic mechanisms and the specific interactions involved in the enzymatic processes aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "ed3f92ca-3821-48e7-be93-af93aeb21555"
      }
    ]
  },
  "18775984": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/18775984.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the biochemical characterization of the enzyme Tgs1, which is involved in the methylation of guanine in RNA caps. The paper mentions the in vitro enzymatic assay to measure the activity of Tgs1, specifically identifying individual amino acids required for its methyltransferase activity. Additionally, it describes the enzyme's function and the biochemical reactions it catalyzes, which are key components of experimental enzymology. The focus on the enzyme's activity and the methods used to analyze it aligns well with the characteristics of an experimental enzymology paper.\n",
        "doc_id": "acd430fb-6d37-4dff-8350-5094c239c6da"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the hTgs1 protein, detailing the methods used to amplify the gene, construct various mutants, and purify the protein using nickel-affinity chromatography. Additionally, it includes a methyltransferase assay to measure the enzymatic activity of the purified hTgs1, which is a key characteristic of experimental enzymology papers. The paper describes the conditions for the enzymatic reaction and the methods used to analyze the results, such as liquid scintillation counting, which further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "00747bc8-3662-4c19-a6c0-854c7f2af09f"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the hTgs1 enzyme, specifically the C-terminal domain hTgs1-(576 – 853), which was produced as a His₁₀Smt3 fusion and purified using Ni²⁺-agarose chromatography. Additionally, the paper details the characterization of the enzyme's methyltransferase activity through an in vitro assay involving the incubation of the enzyme with [³H-CH₃]AdoMet and GpppA, which indicates that the enzymatic activity is being measured. These elements clearly align with the characteristics of experimental enzymology papers, which focus on the overexpression, purification, and activity measurement of enzymes.\n",
        "doc_id": "d5d09856-19e4-4ed5-b4a0-41f25116e5f8"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the hTgs1 enzyme, as well as its enzymatic activity in transferring a methyl group from AdoMet to various substrates, including m⁷GpppA and m⁷GDP. The paper includes details about the conditions under which the enzyme operates, such as optimal pH and substrate specificity, and it presents quantitative data on the enzyme's activity, including turnover numbers and Michaelis-Menten kinetics (Kₘ and kcat values). These elements are characteristic of experimental enzymology, as they involve the measurement of enzyme activity and the characterization of enzymatic reactions.\n",
        "doc_id": "06255014-1ac4-49ad-87bf-af4cf2bd6838"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme hTgs1, as indicated by the mention of \"expressed in bacteria as His₁₀Smt3 fusions and purified from soluble lysates by nickel-agarose chromatography.\" Additionally, it describes in vitro enzymatic assays to measure the activity of the purified enzyme, such as the methyltransferase reactions and the analysis of reaction products using TLC (thin-layer chromatography). The paper provides details on the experimental procedures, including the conditions under which the enzymatic reactions were performed, which is characteristic of experimental enzymology studies.\n",
        "doc_id": "1c8107e3-d79e-4a9a-acff-e97662917ecb"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the hTgs1 protein, as indicated by the mention of \"His₁₀Smt3 fusions, purified by Ni² -agarose chromatography.\" Additionally, it describes in vitro enzymatic assays to measure the activity of the purified enzyme, specifically mentioning \"assayed by protein titration for methyltransferase activity with m⁷GDP as substrate\" and detailing various reaction mixtures and conditions used to analyze the enzyme's activity. The paper also includes kinetic studies and the effects of mutations on enzyme activity, which are typical components of experimental enzymology research.\n",
        "doc_id": "60050a72-8af7-4272-bebc-72dea6bf8a20"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of the hTgs1 enzyme, including the overexpression of its C-terminal catalytic domain. The paper details in vitro enzymatic assays, specifically methyltransferase reactions, to measure the activity of the purified enzyme, as indicated by the mention of reaction mixtures containing specific substrates and the measurement of methyl transfer. The use of SDS-PAGE for analyzing protein preparations and the quantification of enzymatic activity further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "952578be-8257-435f-939d-0bdeba0402b5"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the identification of a minimal catalytic domain of the enzyme hTgs1 that is sufficient for guanine-N² methyltransferase activity in vitro. The paper mentions the use of alanine scanning to identify essential residues for methyltransferase activity, indicating that in vitro enzymatic assays were performed to measure the activity of the enzyme. Additionally, it describes the relationship between the enzyme's structure and its catalytic function, which is a common focus in experimental enzymology studies. The mention of kinetic data and the exploration of the enzyme's active site further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "1f40495f-8171-4eea-bee1-dd75dfcc0352"
      }
    ]
  },
  "8280056": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/8280056.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the production and characterization of catechol O-methyltransferase (COMT), including the overexpression and purification of the enzyme forms (S-COMT and MB-COMT) from rat tissues. The paper mentions the use of Western blotting and Northern blotting techniques to analyze the expression of the enzyme, which indicates that the authors are measuring the activity and presence of the enzyme forms. Additionally, the paper describes the mechanisms of translation initiation and the regulation of the COMT gene, which are relevant to understanding the enzymatic function of COMT. Overall, the focus on enzyme production and characterization aligns with the criteria for an experimental enzymology paper.\n",
        "doc_id": "b8e7441b-40b4-4f22-82d6-a90f22861270"
      }
    ]
  },
  "27387499": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/27387499.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the protein arginine methyltransferase (PRMT) enzymes, specifically focusing on the product specificity of PRMT7 and the structural basis for this specificity. The paper mentions the design of mutations in the active site of the enzyme and analyzes reaction products, which suggests that there are enzymatic assays involved to measure the activity of the mutated enzymes. The mention of high-resolution cation exchange chromatography for analyzing reaction products indicates that the authors are conducting experiments to assess enzyme activity, a key characteristic of experimental enzymology.\n",
        "doc_id": "20f5d50e-a67e-45d5-8415-9a63818427c9"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of the TbPRMT7 enzyme, including the effects of specific mutations on its ability to produce different methylation products (MMA, ADMA, and SDMA). The paper mentions the use of [³H]AdoMet as a cofactor and describes the analysis of hydrolyzed products of arginine methylation, indicating that in vitro enzymatic assays were performed to measure the activity of the enzyme. Additionally, the paper details the generation of double mutants and their impact on enzymatic activity, which is a common approach in experimental enzymology to understand enzyme function and specificity.\n",
        "doc_id": "f07e3be3-459e-4692-8919-df3c0e0a86ff"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the TbPRMT7 enzyme, specifically the E181D/Q329A double mutant, and details the in vitro enzymatic assays used to measure the activity of this purified enzyme. The paper describes the production of SDMA and ADMA from specific peptide substrates, and it includes methods such as TLC analysis and isothermal titration calorimetry to assess enzyme activity and substrate binding affinity. These elements indicate a focus on experimental enzymology, as they involve the characterization of enzyme activity through specific assays.\n",
        "doc_id": "310b182c-59db-43b4-8973-a1a5de1e6c51"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme TbPRMT7, as well as the investigation of its activity and product specificity through in vitro methylation assays. The paper mentions the use of various peptides and the assessment of enzyme activity, including the measurement of methylation products and the effects of active-site mutations on enzyme function. The detailed description of experimental procedures, including the use of chromatography and assays to evaluate enzyme activity, further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "4e75797d-e4aa-43e2-8a2c-4fd76dd5ee94"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro enzymatic activity of various PRMT (protein arginine methyltransferase) mutants and their ability to produce different methylated arginine derivatives when interacting with specific substrates. The mention of \"in vitro methylation\" and \"cation exchange chromatography\" to assess enzyme activity, as well as the detailed analysis of methylated products, indicates that the authors performed enzymatic assays to measure the activity of the purified enzymes. Additionally, the reference to \"Experimental Procedures\" suggests that there are methods described for the overexpression and purification of the enzymes, which is a hallmark of experimental enzymology studies.\n",
        "doc_id": "49698802-23b2-451e-bcdf-b3ab453fa80a"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of various protein arginine methyltransferases (PRMTs), including TbPRMT7 and human PRMT1, which are expressed in E. coli and purified as described in the Methods section. Additionally, the paper mentions the use of peptide substrates for enzymatic assays, indicating that the activity of the purified enzymes is being measured, which is a key characteristic of experimental enzymology. The focus on structural features and mutations affecting enzymatic activity further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "fc6a208f-a07a-4cf6-9e80-40a9bfe82d27"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins (specifically PRMT enzymes) and includes detailed methods for enzymatic assays, such as methylation assays and amino acid analysis. The paper describes the purification process using a HisTrap HP Ni² column, the verification of protein purity through SDS-PAGE, and the conditions under which the enzymatic reactions were performed, including the use of specific substrates and the measurement of enzymatic activity. These elements are characteristic of experimental enzymology studies.\n",
        "doc_id": "f7f1f614-1b39-4c31-8ca7-12d9a35b010e"
      }
    ]
  },
  "28391595": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28391595.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the METTL12 protein, which is a methyltransferase, and details the methods used to express and purify this enzyme from human cells. The paper also mentions the enzymatic activity of METTL12, specifically its role in methylating lysine residues of citrate synthase, indicating that there is an in vitro enzymatic assay involved in measuring the activity of the purified enzyme. The methods section includes information about cell culture, expression of tagged METTL12, and protein analysis, all of which are typical components of experimental enzymology studies.\n",
        "doc_id": "21f940a0-d023-44e4-a8f6-b6e2af75d62f"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the activity of citrate synthase, which is measured using an immunocapture-based microplate assay that quantifies the release of thionitrobenzoic acid in response to the enzymatic reaction. The paper also mentions the purification and characterization of citrate synthase, indicating that the authors have likely overexpressed and purified the enzyme prior to conducting the assay. This focus on enzyme activity measurement and the methods used to assess it aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "73553464-7647-4272-a777-a533bbc21818"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression of the METTL12 protein in HEK293T cells and the subsequent analysis of the methylation of citrate synthase, which is a specific enzymatic activity. The paper details the methods used to identify the methylated sites on citrate synthase through mass spectrometry, indicating that an in vitro enzymatic assay was performed to measure the activity of the modified enzyme. The focus on the methylation of lysine residues in citrate synthase and the comparison of methylation levels in different cell lines further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "59c69c05-b331-4ada-8422-f6058aef7d48"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the methylation of citrate synthase, a key enzyme in the citric acid cycle, and includes details about the enzyme's activity in vitro. Specifically, it mentions that the removal of the methyl group had no effect on the activity of the human enzyme in vitro and compares the specific activity of recombinant porcine citrate synthase lacking the methylation to that of the methylated enzyme. This indicates that the paper involves the purification and activity measurement of an enzyme, which are key components of experimental enzymology.\n",
        "doc_id": "1b886655-c4fd-41ca-9a66-75fc1c514d70"
      }
    ]
  },
  "37137720": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/37137720.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the identification and characterization of two enzymes, METTL7A and METTL7B, which are responsible for thiol methylation activity. The paper mentions the purification of a His-GST–tagged recombinant protein and describes in vitro activity experiments that demonstrate the ability of METTL7A to selectively methylate exogenous thiol-containing substrates. This focus on enzyme purification and activity assays aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "2ce77dea-ac4d-48e4-b992-103a72f87eb4"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL7A protein, which is characterized as a SAM-dependent S-methyltransferase. The paper details the methods used for protein purification, including the use of a His-GST tag and the expression of the protein in E. coli. Additionally, it mentions the biochemical characterization of METTL7A and its enzymatic activity, indicating that in vitro enzymatic assays were performed to measure the activity of the purified enzyme on various thiol-containing substrates. This aligns well with the typical structure and content of experimental enzymology papers.\n",
        "doc_id": "df7cb150-890b-4b18-834c-e484ad0bb0a0"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL7A protein, detailing the methods used for protein expression in E. coli, the purification process using affinity chromatography, and the subsequent in vitro enzymatic assays to measure the methyltransferase activity of the purified METTL7A and METTL7B enzymes. The paper includes specific methodologies for the enzymatic assays, such as the preparation of reaction mixtures, incubation conditions, and the use of mass spectrometry for analyzing the reaction products, which are all characteristic features of experimental enzymology studies.\n",
        "doc_id": "f31e9deb-b9ac-47f5-94b9-840307d93216"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the proteins METTL7A and METTL7B, as indicated by the sections detailing the use of recombinant proteins and the methods for their purification. Additionally, it describes in vitro enzymatic assays to measure the activity of these enzymes, including Michaelis-Menten kinetics and substrate screening assays, which are essential components of experimental enzymology. The paper also includes specific details about the conditions under which these assays were performed, such as the concentrations of substrates and the use of controls, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "a4ecaecc-da38-404b-aa31-81ac711647a8"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL7A enzyme, detailing the use of a pET21 expression plasmid and the purification process involving His-GST tagging and SDS-PAGE analysis. Furthermore, it describes an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically mentioning the methylation activity of N-GST-METTL7A on substrates like captopril and TSL, and the determination of kinetic parameters such as Kₘ and IC₅₀. These elements clearly indicate that the paper focuses on experimental enzymology.\n",
        "doc_id": "847ebc63-6ada-4e1d-8a09-7acecf2271e3"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the proteins METTL7A and METTL7B, as indicated by the mention of \"purified N-GST-METTL7A\" and \"purified recombinant N-GST-METTL7B.\" The paper also describes in vitro enzymatic assays to measure the activity of these enzymes, including the determination of kinetic parameters such as Kₘ for the methyl-donating cofactor SAM and the substrate TSL, as well as competitive inhibition studies. These details clearly point to the experimental enzymology focus of the paper.\n",
        "doc_id": "ded1395a-7622-46e4-89cf-fee1197de924"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL7A and METTL7B proteins, as well as their enzymatic activity in methylation assays. The paper details the use of various assays, including the Promega MTase-Glo assay and LC-MS/MS, to measure the methylation activity of these enzymes on different substrates. Additionally, it describes the effects of specific siRNA treatments on gene expression and subsequent enzymatic activity, which is a common approach in experimental enzymology to understand enzyme function and regulation.\n",
        "doc_id": "7d3421f8-ff29-4362-be71-ab9df7364db6"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzymes METTL7A and METTL7B, which are identified as liver alkyl thiol methyltransferases. The paper includes details about in vitro enzymatic assays, such as the use of the Promega MTase-Glo kit to measure enzyme activity through the formation of S-adenosylhomocysteine (SAH) as an indication of methyl transfer. Additionally, it provides statistical analysis of the enzyme activity and correlation with protein levels, which are typical components of experimental enzymology studies.\n",
        "doc_id": "da22046f-83ad-4e9a-a23c-5c48a7a53058"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the proteins TMT1A and TMT1B, as well as their enzymatic activity in methylating substrates like TSL and other thiol-containing compounds. The paper includes details about kinetic experiments, such as determining the Michaelis constant (Kₘ) for the substrates, and it describes the use of in vitro assays to measure the activity of the enzymes, including the effects of inhibitors like DCMB on TMT activity. These elements are characteristic of experimental enzymology, as they focus on the functional analysis of enzymes and their kinetics.\n",
        "doc_id": "c245bffc-e191-4223-83d1-e5a2d8c41238"
      }
    ]
  },
  "31601797": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31601797.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. The Methods section describes the overexpression and purification of the CcrM protein from *C. crescentus*, detailing the cloning process, bacterial culture conditions, and purification steps using chromatography. Additionally, it mentions the enzyme's activity on double-stranded and single-stranded DNA, indicating that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. This aligns with the characteristics of experimental enzymology papers, which focus on the purification and functional analysis of enzymes.\n",
        "doc_id": "52c27017-a752-40db-bb2c-c412bf82872c"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the protein CcrM, detailing the methods used for purification including the use of HiTrap Q-SP columns and Superdex 200 sizing columns. The paper also describes the conditions under which the protein was crystallized, indicating that the enzymatic activity of the purified enzyme was likely assessed in the context of its interaction with DNA, which is a common focus in enzymology studies. The mention of crystallization and the preparation of the protein for structural analysis further supports its relevance to experimental enzymology.\n",
        "doc_id": "17a77cce-3430-4b83-ae57-631c9d652986"
      }
    ]
  },
  "32747425": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/32747425.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the coronavirus 3C-like protease (3CLpro) and includes details about an in vitro enzymatic assay to measure the activity of the purified enzyme. Specifically, the paper mentions the use of a fluorescence resonance energy transfer (FRET) enzyme assay to evaluate the activity of various inhibitors against the 3CLpro enzymes of MERS-CoV, SARS-CoV, and SARS-CoV-2, which is a key characteristic of experimental enzymology studies.\n",
        "doc_id": "8418ed34-a5d9-4e20-8bc0-b3855aa96974"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the activity of compounds against the 3CLpro enzyme of SARS-CoV-2, including specific IC50 values obtained from enzyme assays. The paper mentions the use of an enzyme assay to measure the activity of the inhibitors against the 3CLpro, which is a key characteristic of experimental enzymology. Additionally, it details the purification and characterization of the enzyme, as well as the interactions of the inhibitors with the enzyme's active site, which further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "c1ad0446-5f17-4c10-b5d0-3369832ecfe1"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the use of an enzyme assay to measure the inhibitory concentrations (IC₅₀ values) of various compounds against the 3CLpro enzyme from different coronaviruses (MERS-CoV, SARS-CoV, and SARS-CoV-2). The mention of the FRET enzyme assay indicates that the authors conducted in vitro enzymatic assays to evaluate the activity of the enzyme in the presence of these inhibitors, which is a key characteristic of experimental enzymology. Additionally, the paper includes details about the interactions between the enzyme and the inhibitors, which further supports its classification as an experimental enzymology study.\n",
        "doc_id": "e6fd5b43-6dd9-4ef2-a229-7ac651ebfb68"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the 3CLpro enzyme from various coronaviruses, including SARS-CoV-2, and describes a FRET enzyme assay to measure the activity of the purified enzyme. The Methods section details the cloning, expression, and purification processes, as well as the specific conditions under which the enzymatic assays were conducted, including the use of substrate and measurement of fluorescence to determine enzyme activity. This aligns well with the characteristics of experimental enzymology papers, which focus on the enzymatic assays and the behavior of purified enzymes.\n",
        "doc_id": "3bef636b-ada0-4572-8bfe-002748140700"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification of SARS-CoV-2 3CLpro, including details on the overexpression and purification process using an E. coli system, and describes the use of various chromatography techniques (Ni-column purification and size exclusion chromatography) to obtain the enzyme. Additionally, the paper mentions crystallization experiments and the generation of enzyme-ligand complexes, which are indicative of enzymatic assays being performed to study the enzyme's activity and interactions with inhibitors. The focus on protein purification and characterization aligns well with the typical content of experimental enzymology papers.\n",
        "doc_id": "2f291615-48a1-4dd8-8d16-d50781634023"
      }
    ]
  },
  "28542609": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28542609.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the identification and characterization of UbV inhibitors that target viral deubiquitinating enzymes (vDUBs), specifically detailing the binding affinities and inhibitory activities of these UbVs against MERS-CoV PLpro and CCHFV OTU. The paper mentions the use of fluorogenic substrates (Ub-AMC and ISG15-AMC) to measure the deubiquitinating and deISGylating activities of the enzymes, which is a clear indication of an in vitro enzymatic assay. Additionally, the methods include the screening of a phage-displayed library and the determination of binding affinities using techniques like enzyme-linked immunosorbent assays and Bio-Layer Interferometry, all of which are typical components of experimental enzymology studies.\n",
        "doc_id": "95dbb1ce-630a-456f-b02c-cd9b7d3a159a"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the inhibition of viral deubiquitinating enzymes (DUBs) by UbV inhibitors, which involves the measurement of enzymatic activity. The paper describes the use of Ub-AMC and ISG15-AMC as substrates in dose-response curves to determine the IC₅₀ values, indicating the concentration of UbV that reduces proteolytic activity by 50%. Additionally, it mentions the incubation of purified MERS-CoV PLpro and CCHFV OTU with UbV inhibitors and biotinylated tetra-Ub substrates, followed by detection of proteolytic activity through Western blotting. These details point to the experimental enzymology focus of the paper, as it involves the purification of enzymes and the assessment of their activity in vitro.\n",
        "doc_id": "f8ebd0a0-bfb1-4a1e-a6ff-89453329bed4"
      }
    ]
  },
  "29149603": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/29149603.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 13,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of various constructs of human proteins (such as mtRNAP and TFB2M) with specific modifications, including the addition of tags for purification. The Methods section indicates the use of Escherichia coli strains for recombinant expression, which is a common practice in experimental enzymology. Additionally, the mention of constructing protein variants and the use of techniques like limited proteolysis and Edman sequencing suggests a focus on characterizing the proteins, which is often a precursor to conducting enzymatic assays to measure activity.\n",
        "doc_id": "4043faad-9004-4d8a-b578-7d9180c578a3"
      },
      {
        "page": 14,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of several proteins, including human mtRNAP and TFAM, using methods such as affinity chromatography and size exclusion chromatography. The detailed description of the protein expression conditions, purification steps, and the use of specific buffers indicates a focus on preparing these proteins for further enzymatic assays. Although the paper does not explicitly mention enzymatic assays in the provided text, the context suggests that the purified proteins are intended for such assays, which is a common practice in experimental enzymology.\n",
        "doc_id": "e7b9ccf9-882c-45e1-af7c-5fc8c9fd3205"
      }
    ]
  },
  "31913360": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31913360.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the characterization of the METTL4 enzyme, including its overexpression and purification, and details an in vitro enzymatic assay to measure its activity on RNA substrates. Specifically, the paper describes how recombinant METTL4 was incubated with RNA substrates in the presence of stable isotope-labeled S-adenosylmethionine to assess its methylation activity, which is a key aspect of experimental enzymology. The results demonstrate the enzyme's specificity and activity, aligning with the typical focus of experimental enzymology papers on enzyme assays and characterization.\n",
        "doc_id": "259f5372-35e9-45bf-89fa-4ceac1a3b987"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of METTL4, including the determination of the Michaelis constant (Kₘ) for the enzyme's activity on a specific RNA substrate. The paper mentions the intrinsic enzymatic activity of METTL4 and how a catalytic mutation affects its ability to methylate RNA, which indicates that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. This aligns with the characteristics of experimental enzymology papers that focus on enzyme activity and kinetics.\n",
        "doc_id": "3af30704-d36f-4716-8d5b-f3712692eb2b"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the characterization of METTL4 as an internal m6Am methyltransferase, including the measurement of its enzymatic activity towards different RNA substrates in vitro. The paper mentions the determination of Michaelis–Menten kinetics for recombinant METTL4, which is a key aspect of experimental enzymology. Additionally, it describes the overexpression and purification of the enzyme, as well as the use of in vitro assays to assess its activity, which are all hallmarks of experimental enzymology studies.\n",
        "doc_id": "0a61a6ba-bef3-4b08-8332-039b35b6fd1e"
      }
    ]
  },
  "28520920": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28520920.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the investigation of a human methyltransferase (KMT) that methylates a specific lysine residue in the eukaryotic elongation factor 1 alpha (eEF1A). The authors mention combining in vitro enzymology with analyses of knockout cells, which indicates that they performed enzymatic assays to measure the activity of the purified enzyme. Additionally, they demonstrate the importance of a specific sequence motif in the active site for catalytic activity, which is a key aspect of experimental enzymology. The focus on the enzymatic activity and the characterization of the methyltransferase aligns well with the criteria for an experimental enzymology paper.\n",
        "doc_id": "b0652e82-8183-4cb2-8249-04ee47cfeba5"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The authors describe the characterization of a new human methyltransferase (MTase) that specifically methylates lysine residues in the eukaryotic translation elongation factor 1 alpha (eEF1A). They detail the purification of the recombinant enzyme and demonstrate its enzymatic activity in vitro, specifically showing that eEF1A-KMT4 catalyzes the methylation of K36 in recombinant eEF1A. The paper includes methods for gene cloning, mutagenesis, and the generation of knockout cell lines, which are all indicative of experimental work focused on enzymatic assays and protein characterization.\n",
        "doc_id": "23cf14ad-ef48-41a7-8032-a4676553f7de"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the expression and purification of recombinant proteins, specifically mentioning the use of a hexahistidine (His6) tag for purification from bacteria, which is a common practice in enzymology to obtain active enzyme for assays. Additionally, the paper describes the preparation of cellular extracts for in vitro methylation assays, indicating that enzymatic activity is being measured. The methods outlined suggest a focus on the enzymatic properties and activities of the proteins being studied, which aligns with the characteristics of experimental enzymology papers.\n",
        "doc_id": "c698043f-a1b0-403c-a8d9-caa1ec58c33a"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of a protein/enzyme, specifically mentioning the use of iso-propyl b-D-1-thiogalactopyranoside for inducing protein expression, and details the purification process using nickel nitrilotriacetic acid-agarose. Additionally, it describes in vitro methyltransferase (MTase) assays to measure the activity of the purified enzyme, including the conditions for the assays and the methods used for analyzing the results, such as SDS-PAGE and mass spectrometry. These elements clearly indicate that the paper focuses on experimental enzymology.\n",
        "doc_id": "6a48715d-9f6a-4ff0-b3e3-dffc30cea1a8"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The text discusses the overexpression and purification of the eEF1A-KMT4 protein, detailing the methods used for protein purification, including the use of affinity resin and subsequent analysis by mass spectrometry. Additionally, it describes an in vitro enzymatic assay where the methylation activity of the purified enzyme is measured using recombinant eEF1A-KMT4 and [3H]AdoMet, along with the effects of ATP on the methylation process. This focus on enzyme activity and the methods to assess it aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "c861b523-5c58-40d4-bc6d-26e55f9ed054"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of eEF1A-KMT4, including the identification of substrates and the effects of mutations on enzymatic activity. The methods section describes the use of protein extracts and recombinant proteins in methylation reactions, which are indicative of in vitro enzymatic assays. Additionally, the paper details the purification and analysis of proteins through chromatography and SDS-PAGE, which are common techniques in experimental enzymology to study enzyme function and activity.\n",
        "doc_id": "e77c477f-69b3-49c4-af1b-340937c03c93"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme eEF1A-KMT4, as well as the in vitro enzymatic assays that measure the methylation activity of this enzyme on its substrates, eEF1A1 and eEF1A2. The methods section describes the use of recombinant proteins, the conditions under which the methylation reactions were performed, and the quantification of methylation activity through liquid scintillation counting, which are all key components of experimental enzymology.\n",
        "doc_id": "a2b6d683-8db0-4412-bd54-e2c64ea427d7"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme eEF1A-KMT4, and it details an in vitro enzymatic assay where the enzyme is shown to methylate specific lysine residues on eEF1A proteins. The methods include the treatment of recombinant eEF1A1 with eEF1A-KMT4 and AdoMet, followed by analysis of the resulting peptides, which confirms the enzymatic activity of eEF1A-KMT4. The paper also provides evidence of the enzyme's specificity and activity through mutational analysis, further supporting its classification as an experimental enzymology study.\n",
        "doc_id": "ae773347-1408-486d-8b17-f23d60815f7d"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the investigation of the functional importance of a conserved sequence motif in the enzyme eEF1A-KMT4, specifically detailing how mutations in this motif affect the enzymatic activity of the enzyme on a substrate (recombinant eEF1A1). The paper mentions assaying the activity of mutant enzymes, which indicates that in vitro enzymatic assays were performed to measure the activity of the purified enzyme, a key characteristic of experimental enzymology.\n",
        "doc_id": "e5b70fdf-056b-4573-8fa8-8f9504cf3a76"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the identification and characterization of a protein family of eEF1A-KMT4-like KMTs, including details about mutational analysis of the enzyme and its activity. Specifically, it mentions \"mutant eEF1A-KMT4 proteins with single amino acid substitutions in motif Post II were tested for MTase activity on recombinant eEF1A1,\" which indicates that an in vitro enzymatic assay was performed to measure the activity of the purified enzyme. This aligns with the typical characteristics of experimental enzymology papers, which include the overexpression, purification, and activity measurement of enzymes.\n",
        "doc_id": "95ae98d0-b1f4-44cf-bcc8-f11b46b7cc73"
      }
    ]
  },
  "7896706": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/7896706.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the measurement of specific enzyme activities, such as P(N/M)P oxidase, and includes details about the purification and characterization of enzymes involved in the biosynthesis of vitamin B6. The paper mentions the use of various biochemical methods, including assays to measure enzyme activity (e.g., \"P(N/M)P oxidase was measured by a previously described method\"), which indicates that it involves experimental enzymology. Additionally, the paper describes the growth conditions and the effects of mutations on enzyme activity, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "6adae586-3c7d-49d4-a4c8-ac206389b29b"
      }
    ]
  },
  "32820242": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/32820242.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Laetiporus polyketide synthase LpaA, detailing the construction of expression vectors and transformation of Aspergillus species. The paper also describes the purification of laetiporic acids and includes methods for growth inhibition assays, which involve measuring the activity of the produced compounds. The mention of enzymatic assays, such as the quantification of polyenes and the use of HPLC for analysis, indicates that the paper is focused on experimental enzymology.\n",
        "doc_id": "26f7cf3c-f25b-41a6-9b25-6d95349e18ce"
      }
    ]
  },
  "19292762": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/19292762.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a protein (6xHis-tagged ubiquitin) in transgenic plants, which is a key aspect of experimental enzymology. The methods section indicates the use of affinity chromatography for purification, and the results include biochemical analyses that suggest the activity of the ubiquitin protein in vivo, such as its incorporation into poly-Ub chains and conjugates. The paper also implies the use of enzymatic assays to measure the effects of the ubiquitin modifications on plant growth and protein turnover, which aligns with the typical focus of experimental enzymology on enzyme activity and function.\n",
        "doc_id": "f720eb9f-f621-41e6-b103-89cc810aa731"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a protein (6His-UBQ) and describes the use of affinity chromatography techniques (GST–UBA and Ni–NTA chromatography) to enrich for ubiquitylated proteins. The methods section indicates that the authors performed in vitro assays to analyze the activity of the purified proteins, specifically mentioning the immunoblot analysis with anti-Ub antibodies and the detection of Ub conjugates following SDS–PAGE. This focus on protein purification and enzymatic activity measurement aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "9f56b981-1fcd-4f89-86cb-0a31c17e5885"
      },
      {
        "page": 13,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins, specifically the UBA1 and 2 domains of human HHR23A protein fused to GST, and describes the methods used for purification, including the use of glutathione Sepharose 4B. Additionally, the paper mentions enzymatic assays and analysis techniques such as immunoblotting and mass spectrometry, which are commonly associated with experimental enzymology studies. The detailed methodology for protein purification and subsequent analysis indicates a focus on enzymatic activity and protein interactions, characteristic of experimental enzymology research.\n",
        "doc_id": "d3aabdee-c2c2-4365-921a-9ceff00ca0b5"
      }
    ]
  },
  "22095282": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/22095282.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. The authors discuss the in vitro methylation assay where they investigate the methylation of ASK1 by PRMT1, detailing the experimental setup including the use of GST-tagged proteins and [³H]SAM as the methyl donor. They describe the purification and interaction of the proteins involved, as well as the specific residues being methylated, which are key components of experimental enzymology. The paper also includes results from various assays that measure the enzymatic activity of PRMT1 on ASK1, confirming its role as a methyltransferase.\n",
        "doc_id": "40fb9df9-948e-4c41-ada0-5ab022f05f87"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the enzyme PRMT1 on the substrate ASK1, which is a clear indication of an enzymatic assay. The paper details the methods used to assess this activity, including the use of immunoprecipitation (IP) and immunoblot analysis (IB) to analyze the interaction and activity of the proteins involved. Additionally, it describes the experimental setup where recombinant GST-PRMT1 is incubated with GST fusion proteins of ASK1 deletion mutants, and the resulting methylation activity is measured, which aligns with the characteristics of experimental enzymology.\n",
        "doc_id": "6d21b5ea-f7bc-408f-b1ba-9ae46b2a6a2d"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the examination of ASK1 activity through immune complex kinase assays, which are a type of in vitro enzymatic assay used to measure the activity of the ASK1 enzyme. The paper details the methods used to assess ASK1 activity, including the use of specific substrates (GST-MKK6 and GST-c-Jun) and the immunoprecipitation techniques employed to isolate the enzyme for activity measurement. Additionally, the paper mentions the overexpression of ASK1 and its interaction with PRMT1, which aligns with the typical focus of experimental enzymology on protein/enzyme purification and activity assays.\n",
        "doc_id": "2a7d6016-4602-4201-872b-f4ce6f6a0613"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins, specifically PRMT1 and ASK1, and includes detailed methodologies for in vitro assays, such as the in vitro methylation assay and immune complex kinase assay. The paper describes the use of S-adenosyl-L-[methyl-³H]methionine for methylation reactions and the quantification of substrate phosphorylation, which are key components of enzymatic assays. Additionally, the methods section outlines the purification of proteins and the conditions under which these assays were performed, indicating a focus on enzymatic activity and regulation.\n",
        "doc_id": "b849a102-b779-4fb0-8514-6e7476b4751e"
      }
    ]
  },
  "30197297": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/30197297.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the reconstitution of methyltransferase activity in vitro, specifically mentioning the catalytic activity of the METTL16 enzyme on the MAT2A mRNA. The paper details the purification and crystallization of the METTL16 protein, as well as its interaction with RNA, which are key components of experimental enzymology. Additionally, it describes the use of size-exclusion chromatography and multi-angle static light scattering to analyze the enzyme's properties, indicating a focus on the enzyme's activity and function in a controlled experimental setting.\n",
        "doc_id": "72f09873-3ca0-40f4-9426-832c3fe9f609"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of METTL16 and METTL3/METTL14, including the effects of RNA substrate mutations on enzymatic activity. The paper mentions performing enzymatic assays to measure the activity of the enzymes with specific RNA substrates, which is a key characteristic of experimental enzymology. Additionally, it describes the structural interactions between the enzymes and their RNA substrates, which is relevant to understanding their catalytic mechanisms.\n",
        "doc_id": "a1687131-4f30-4386-a2b8-4ba2d632b50c"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the enzyme METTL16 on various RNA substrates, indicating that enzymatic assays were performed to measure the activity of the purified enzyme. The paper mentions specific experimental results, such as the incorporation of tritium into methylated RNA substrates and the effects of mutations on methylation activity, which are typical features of experimental enzymology studies. Additionally, the paper describes the structural context and interactions that influence the enzyme's activity, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "b22fe721-7b35-44ac-87ef-7a98f65bcf8c"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the METTL16 enzyme on various RNA substrates, which indicates that enzymatic assays are being performed to measure the activity of the enzyme. The paper provides data on the methylation efficiency of METTL16 on different RNA hairpins and chimeras, and it mentions the comparison of wild type METTL16 with variants containing point mutations, all of which are typical elements found in experimental enzymology studies. The focus on the enzyme's activity and the conditions under which it operates further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "135f2504-db13-445c-b821-b5d7bcde0601"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of the METTL16 protein, specifically focusing on its methyltransferase activity. The paper details how mutations in specific residues affect the enzyme's activity, indicating that in vitro assays were performed to measure these effects. For instance, it mentions testing mutations that interfere with cofactor binding and how these mutations abrogate or enhance methyltransferase activity, which is a clear indication of an enzymatic assay being conducted. Additionally, the paper describes the effects of various mutations on the methylation efficiency of METTL16, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "5daedf04-3c22-442b-acb8-886b9342cd95"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity of the METTL16 enzyme on RNA substrates, which is a clear indication of an enzymatic assay being performed. The paper includes details about the effects of various mutations on the enzyme's activity, as well as data presented from these assays (e.g., \"In vitro methylation activity of wild-type or mutant METTL16 on hp1\" and \"Data are shown as mean DPM ± SD from three replicates\"). This focus on measuring the enzymatic activity of a purified enzyme aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "9ec2be19-1350-4f41-a70f-24b7e4e623f0"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the METTL16 protein, as indicated by the mention of \"Expression of recombinant proteins\" and \"Protein purification\" in the Methods section. Additionally, it includes an \"in vitro methylation assay,\" which is a key component of experimental enzymology, as it measures the enzymatic activity of the purified enzyme. The paper also describes the regulatory mechanisms of METTL16 and its interaction with RNA substrates, which are relevant to understanding the enzyme's function and activity.\n",
        "doc_id": "918cdfc7-bae4-41d1-a132-6e1f085a77de"
      },
      {
        "page": 14,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of recombinant proteins, specifically METTL16 constructs, which is a key aspect of experimental enzymology. The methods section details the transformation of plasmids into E. coli, the expression of target proteins, and the purification process using affinity chromatography and ion-exchange chromatography. Although the excerpt does not explicitly mention an in vitro enzymatic assay, the focus on protein purification and the context suggest that the paper is likely to include enzymatic activity measurements in the full text.\n",
        "doc_id": "4106c4bd-3074-49d9-b943-54bc1dd88707"
      },
      {
        "page": 15,
        "text": "\nYes: this paper is a good example of an enzymology paper. It includes a detailed description of an in vitro methylation assay, which is a type of enzymatic assay used to measure the activity of the METTL16 enzyme. The methods section outlines the components of the reaction mixture, the conditions under which the assay was performed, and the techniques used to analyze the results, such as liquid-scintillation counting to quantify the incorporation of the methyl group into RNA. This focus on enzyme activity measurement and the purification of the enzyme indicates that the paper is centered around experimental enzymology.\n",
        "doc_id": "363a604e-6484-421d-a8c6-474fbd0d307c"
      }
    ]
  },
  "17322287": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/17322287.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins, specifically mentioning the transfer of clones to a bacterial expression vector, induction of expression, and purification of the proteins. Additionally, it describes the use of these purified proteins in assays, such as protein-binding microarrays (PBM), to identify DNA sequence motifs bound by the proteins. The focus on protein expression and purification, along with the application of these proteins in functional assays, aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "7d150bad-5d88-4441-ad47-d6559b98d033"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins, specifically mentioning the purification of Rap1 expressed in E. coli and S. cerevisiae. The methods section describes the use of GST affinity purification and the robotic protocols for protein purification, which are key components of experimental enzymology. Additionally, the paper details the use of protein-binding microarray experiments, which involve measuring the activity of the purified protein, indicating that enzymatic assays are part of the study.\n",
        "doc_id": "2a955d19-eb1f-486d-acc2-5f7ac4776d16"
      }
    ]
  },
  "31666994": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31666994.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the bergaptol O-methyltransferase (PpBMT) enzyme, as well as the use of site-directed mutagenesis to create high-activity mutants. The paper mentions the determination of crystal structures and the identification of key amino acids involved in substrate binding, which are typical components of experimental enzymology. Additionally, it describes the production of bergapten from bergaptol using the engineered enzyme, indicating that enzymatic activity was measured and analyzed, which is a core aspect of experimental enzymology.\n",
        "doc_id": "7cab6350-b0c8-4178-8434-1024683b6755"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the bergaptol-specific O-methyltransferase (PpBMT) protein, detailing the methods used for protein expression in E. coli and purification using glutathione S-transferase-conjugated affinity resin. Additionally, the paper includes a section on enzymatic activity assays, where the activity of the purified enzyme is measured under various conditions, which is a key characteristic of experimental enzymology. The study also explores the catalytic mechanism and the effects of mutations on enzyme activity, further emphasizing its focus on enzymatic assays and protein functionality.\n",
        "doc_id": "998925a5-44a6-43a4-9553-06db06f6efe9"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of a protein/enzyme (PpBMT V320I) and includes an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically mentioning the analysis of cellular tyrosinase (TYR) activity and melanin content in B16F10 melanoma cells. The methods section describes the use of polymerase chain reaction for site-directed mutagenesis, transformation into E. coli for protein expression, and subsequent enzyme-activity analysis, which are all key components of experimental enzymology.\n",
        "doc_id": "15c15844-2990-46a2-a05a-b35d0b948dbe"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The text discusses the overexpression and purification of the enzyme PpBMT, as well as the use of site-specific mutagenesis to improve its catalytic activity. It details the methods used to analyze the enzyme's structure and binding sites, and it describes the enzymatic activity of various mutants, indicating that in vitro assays were performed to measure the activity of the purified enzyme. The focus on improving enzymatic activity through protein engineering and the mention of producing bergapten using the engineered enzyme further support its classification as an experimental enzymology paper.\n",
        "doc_id": "2262e5c7-ffae-4401-b5c3-58e98acfe16b"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the measurement of tyrosinase (TYR) activity, which is a key enzymatic assay. The paper mentions that TYR activities were measured in terms of L-DOPA oxidation using lysates obtained from B16-F10 cells after treatment with bergapten. This indicates that the study involves the purification and activity measurement of an enzyme, which is characteristic of experimental enzymology. Additionally, the paper includes details about melanin content and the effects of bergapten on these enzymatic activities, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "105d9f3c-8fbc-4d76-99ad-fdc0ac52faaa"
      }
    ]
  },
  "19717466": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/19717466.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the functional characterization of the tRNA-wybutosine synthesizing enzyme (TYW2) and includes details about in vitro assays, such as mass spectrometric and radioisotope-labeling analyses, to confirm the enzymatic activity of TYW2 in transferring the acp group from AdoMet to its substrate. The paper also mentions kinetic analyses, which are typical in experimental enzymology to measure enzyme activity. Additionally, the structural analysis of the enzyme and its interaction with AdoMet further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "15537cc2-bd76-477c-b301-32cbd9352037"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The text describes the overexpression and purification of the PhTYW2 and MjTYW2 proteins, which are archaeal homologs of a yeast enzyme involved in tRNA modification. It details in vitro reconstitution assays to measure the acp-group transfer activity of these enzymes, including the use of mass spectrometry to analyze the products formed during the enzymatic reaction. Additionally, it mentions the use of a radio-labeled substrate to quantify the incorporation of the acp group, which is a clear indication of an enzymatic assay being performed to assess enzyme activity.\n",
        "doc_id": "a01dd699-bf25-4d03-8717-9cb3dcdc9b77"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro activity of Ala mutants of specific residues (Asp-183 and Glu-155) in the context of the enzyme PhTYW2, indicating that the authors performed enzymatic assays to measure the activity of these mutants compared to the wild-type enzyme. The mention of monitoring the incorporation of the [¹⁴C]acp group donated from AdoMet further confirms that the paper includes experimental enzymology, as it involves the measurement of enzymatic activity, which is a key aspect of experimental enzymology studies.\n",
        "doc_id": "521c5607-528d-4582-994f-63cb21097f46"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the structural comparison of the enzyme PhTYW2 and its interaction with AdoMet, including details about the enzyme's active sites and the specific residues involved in substrate binding and catalysis. The mention of \"acp-group transfer activity\" and the evaluation of \"relative activities to the wild-type enzyme\" indicates that there are enzymatic assays being performed to measure the activity of the enzyme, which is a key characteristic of experimental enzymology. Additionally, the paper describes the structural determinants for the acp-group transfer, which further emphasizes the focus on enzymatic function and activity.\n",
        "doc_id": "4dbb03d3-0e8f-486b-9752-99d06acd7787"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the preparation of Ala mutants of specific residues to analyze their acp-transfer activities, indicating that in vitro enzymatic assays were performed to measure the activity of the enzyme. The paper also mentions the use of a reconstitution assay to demonstrate the activity of archaeal TYW2 with yeast tRNA, which further supports the experimental nature of the work. Additionally, the paper provides details on the mutations that affect enzymatic activity, which is a common focus in experimental enzymology studies.\n",
        "doc_id": "42fd0dfd-b279-4a8c-92bb-5b330abe90ca"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins (specifically, archaeal TYW2) in Escherichia coli, which is a common method in enzymology studies. The paper also describes in vitro reconstitution assays that demonstrate the enzymatic activity of TYW2, specifically its ability to form yW-86 from imG-14 in tRNA. Additionally, it mentions the measurement of acp-transfer activity using LC/MS analysis and a standard filter binding assay, which are typical methods used to assess enzyme activity. These details indicate that the paper focuses on experimental enzymology, particularly the characterization of enzyme activity and the methods used to study it.",
        "doc_id": "987932af-0947-4156-a098-f3f86f4bb110"
      }
    ]
  },
  "30988178": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/30988178.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the identification and characterization of phenoloxidase (PO) as a predominant protein in the body fluid of soldier nymphs of Nipponaphis monzeni. The paper includes an enzymatic activity assay that detected high PO activities, which is a key aspect of experimental enzymology. Additionally, it mentions the purification and molecular cloning of the PO cDNA, indicating a focus on the biochemical properties and functions of the enzyme, which aligns with the typical structure and content of experimental enzymology papers.\n",
        "doc_id": "aff3e951-55c9-4572-91f5-6a917a928de1"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text mentions the measurement of phenoloxidase (PO) activity in soldier’s body fluid and whole body extracts, which indicates that there are enzymatic assays being performed to assess the activity of the purified enzyme. Additionally, the paper discusses the purification and characterization of proteins, including the use of SDS/PAGE and immunoblotting, which are common techniques in experimental enzymology to analyze proteins and their activities. The focus on protein expression levels and evolutionary aspects of the PO gene also aligns with the themes typically explored in enzymology research.\n",
        "doc_id": "ad28b68f-bafb-4675-8432-7e95aa2ebdf6"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins, specifically recombinant phenoloxidase (PO) and repeat-containing protein (RCP), using insect cells and E. coli, respectively. The paper also describes an in vitro clotting assay that measures the activity of these purified enzymes in the context of the PO-mediated melanin synthesis pathway. The experimental details, such as the concentrations of the proteins used in the assays and the results of the clot formation, indicate that the authors conducted enzymatic assays to assess the functionality of the proteins they purified.\n",
        "doc_id": "7ec50460-a235-44ad-9d97-23a3f54e9be3"
      }
    ]
  },
  "20382657": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/20382657.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification of recombinant enzymes (PAB0505 and PAB2272) and describes the tRNA:m1G37 methyltransferase activity assays conducted with these purified enzymes. The methods section details the incubation of the enzyme with various tRNA substrates and the use of radiolabeled compounds to measure enzymatic activity, which are key components of experimental enzymology. The paper also mentions the preparation of substrates and the conditions under which the enzymatic reactions were performed, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "508d560e-00c3-47b2-84e8-64fa6248e919"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification and characterization of recombinant enzymes (Trm5a and Trm5b) and their ability to catalyze the methylation of tRNA in vitro. The paper details the use of specific substrates (bulk tRNA from various strains) and the measurement of enzymatic activity through thin layer chromatography of radiolabeled tRNA hydrolysates, which is a typical method used in enzymatic assays to assess enzyme activity. The results indicate differences in the enzymatic activities of the two proteins, further supporting its classification as an experimental enzymology study.\n",
        "doc_id": "c95219a7-8603-4ac3-8d5e-71edc475d3b5"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of the recombinant enzyme Trm5a from Pyroc. abyssi, which is involved in the methylation of imG-14 in tRNA. The paper details an in vitro assay where the enzyme is incubated with [14C-methyl]-S-AdoMet to measure its activity in catalyzing the formation of methylated nucleotides. This experimental approach, including the use of radioactive labeling and TLC analysis to confirm the enzymatic activity, aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "0d965bda-419f-45ac-91b5-0aa6058e53ac"
      },
      {
        "page": 13,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro analysis of Trm5 enzymes, specifically mentioning the ability of Pyrococcus abyssi Trm5a to methylate a specific substrate (C7 of imG-14). The paper references previous studies that have experimentally shown the methyltransferase activity of related enzymes, indicating that the authors are conducting enzymatic assays to measure the activity of the purified enzymes. Additionally, the mention of conserved residues involved in substrate binding and the comparison of different Trm5 family members suggests a focus on the enzymatic function and characteristics of these proteins, which is a hallmark of experimental enzymology.\n",
        "doc_id": "10c5899f-5ccb-4c85-8f98-93b94b3b14f9"
      }
    ]
  },
  "35336895": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/35336895.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the PDCoV Mpro enzyme, detailing the methods used for purification such as Ni-affinity chromatography and anion exchange chromatography. Additionally, it includes a section on enzyme activity and inhibition assays, where the activity of the purified enzyme is measured using a fluorogenic substrate, which is a key characteristic of experimental enzymology papers. The paper also provides specific details about the assay conditions and the determination of kinetic parameters (Km, kcat, Ki, and k3), further emphasizing its focus on enzymatic activity.\n",
        "doc_id": "e453fddb-5ba4-4280-a4c8-6b90789eaf6e"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the determination of kinetic parameters (Km and kcat) for the PDCoV Mpro enzyme, which are essential aspects of enzymatic assays. The paper also mentions an enzymatic assay that shows how the peptidomimetic inhibitor N3 inactivates PDCoV Mpro, providing specific values for Ki and k3, which further indicates the measurement of enzyme activity. The detailed analysis of the enzyme's substrate-binding pocket and the interactions with the inhibitor also align with the experimental enzymology focus on enzyme characterization and inhibition studies.\n",
        "doc_id": "2d296d9e-a44c-4f39-b02d-1760cc4d20c2"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the evaluation of the inhibitory activity of various compounds against the PDCoV Mpro enzyme, including specific inhibition ratios and kinetic parameters (k3/Ki values). The paper mentions the design of peptidomimetic inhibitors and their interactions with the enzyme, indicating that there are in vitro enzymatic assays being performed to measure the activity of the enzyme in the presence of these inhibitors. The detailed analysis of the interaction between the enzyme and the inhibitors, along with the mention of enzymatic activity, clearly aligns with the characteristics of an experimental enzymology paper.\n",
        "doc_id": "16a95420-d427-45d7-829d-0cdbe02753d3"
      }
    ]
  },
  "25133732": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/25133732.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of specific enzymes (CaXMT1 and TCS1) involved in the caffeine biosynthetic pathway, detailing the construction of expression vectors and the transformation into E. coli for protein production. The methods section describes the use of PCR for cloning, the induction of protein expression, and the preparation of a crude enzyme mix for subsequent assays, which indicates that enzymatic activity related to caffeine metabolism is being measured. This aligns well with the characteristics of experimental enzymology papers, which typically include the purification of enzymes and in vitro assays to assess their activity.\n",
        "doc_id": "4d457e61-4c54-476e-b7a2-70dbf65992e7"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the cloning and expression of caffeine biosynthetic enzymes in E. coli, as indicated by the mention of oligonucleoside primers for PCR used for cloning and expression. Additionally, it includes details about the expression of recombinant proteins, such as GST and CaXMT1-GST fusion proteins, which are typically purified and assayed for enzymatic activity. The mention of SDS-PAGE analysis to visualize the expression of these proteins further supports that this paper is focused on experimental enzymology, as it implies that the authors are likely assessing the activity of these enzymes in subsequent assays.\n",
        "doc_id": "f70ac5bd-986e-42d2-9082-ecb91f21fba9"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the proteins CaXMT1 and TCS1, as well as their enzymatic activity in vitro. The paper details the methods used for enzymatic assays, including the use of crude GST-fusion protein extracts and the specific substrates involved in the reactions. Additionally, it describes the analysis of reaction products using HPLC and mass spectrometry, which are common techniques in experimental enzymology to measure enzyme activity. The presence of these elements indicates that the paper focuses on experimental enzymology.\n",
        "doc_id": "084bae86-772f-486c-9416-97aa193109bd"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins (specifically nucleosidase candidate genes) in yeast, as well as the functional analysis of these proteins. The methods section describes the use of yeast assays, the extraction of compounds from culture media, and the analysis of these compounds using HPLC and LC-MS, which are indicative of enzymatic assays. Additionally, the paper mentions the use of SDS-PAGE to analyze recombinant proteins, further supporting its focus on enzymatic activity and protein characterization.\n",
        "doc_id": "ae489cb7-45b6-4818-913b-99df5c9df336"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the cloning and functional analysis of key enzymes involved in caffeine biosynthesis, specifically mentioning the overexpression and purification of the enzymes CaXMT1 and TCS1 in E. coli. The paper details the in vitro analysis of enzymatic reactions, including the incubation of crude fusion protein extracts and the use of HPLC to determine the reaction products, which are key components of experimental enzymology. The methods section describes the use of expression vectors and the transformation of E. coli, indicating a focus on enzyme activity and characterization.\n",
        "doc_id": "33f9b311-2cff-490d-8ef0-047811ed8160"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of enzymes (CaXMT1 and TCS1) in E. coli and yeast, and it includes detailed descriptions of in vitro enzymatic assays to measure the activity of these enzymes. The paper mentions the use of HPLC to analyze the products of the enzymatic reactions, confirming the enzymatic activities of the expressed proteins. Additionally, it describes the conditions under which the assays were performed, including the substrates used and the results obtained, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "65a807ca-7cd9-44ad-bd08-fabe0d64dba3"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of a protein/enzyme (TCS1) in E. coli, as indicated by the mention of HPLC analysis of enzymatic reaction products and the use of specific vectors for protein expression. The paper also hypothesizes about the role of nucleosidases in caffeine biosynthesis, which suggests that enzymatic assays were performed to measure the activity of the purified enzyme. The focus on enzymatic reactions and the analysis of products further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "a91a0777-129b-42b2-9d74-36a9955ad811"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins (TCS1 and ICS1) in E. coli, and it includes details about enzymatic assays to measure the activity of these proteins towards specific substrates (7-MX and SAM). The paper also presents HPLC analysis of the enzymatic reactions, which is a common method used to assess enzyme activity, indicating that the authors are measuring the products of these reactions. The mention of co-expression and functional analysis further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "7236281f-6ca2-41ed-bfcf-7ea60c04e601"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of enzymes (TCS1 and CaXMT1) and their enzymatic activity in vitro, specifically measuring the production of caffeine and theobromine. The paper details the methods used for co-expressing these enzymes in E. coli, the optimization of reaction conditions, and the use of HPLC to determine the enzymatic activity, which are all key components of experimental enzymology. Additionally, it mentions site-directed mutagenesis to alter enzyme activity, further emphasizing the experimental approach to studying enzyme function and activity.\n",
        "doc_id": "c6f1865c-2f8c-480b-bafc-35bd9f4c16b6"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of caffeine synthase from tea leaves, which indicates that the authors likely performed an enzymatic assay to measure the activity of this enzyme. The mention of \"N-methyltransferases\" and their roles in the caffeine biosynthetic pathway suggests that the paper involves the study of enzyme activity and function, which is a key aspect of experimental enzymology. Additionally, the focus on metabolic engineering and the biosynthesis of caffeine implies that the authors are investigating the enzymatic processes involved in this pathway.",
        "doc_id": "107fbf57-b885-4fab-a5eb-39878c02dbb8"
      }
    ]
  },
  "11836534": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/11836534.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the methyl transfer activity of various Dnmt3b2 fragments, indicating that the authors performed in vitro assays to measure the enzymatic activity of the purified enzyme on different DNA substrates. The mention of \"methyl transfer activity,\" \"unmethylated (CpG) and hemimethylated (hemi-CpG) oligonucleotide substrates,\" and the comparison of activities with a positive control (Dnmt1) all point to the performance of enzymatic assays, which is a hallmark of experimental enzymology. Additionally, the paper describes the expression of Dnmt3b2 proteins in E. coli, which suggests that the authors likely overexpressed and purified the enzyme for their assays.\n",
        "doc_id": "18681355-5a4d-4b6c-9d8a-1fa32d97fbd2"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The Methods section describes the expression and purification of the Dnmt3b2 protein, which is a key aspect of experimental enzymology. It details the use of E. coli for protein expression, the induction conditions, and the purification techniques employed (chelated-nickel, ion-exchange, and gel filtration columns). Additionally, the paper mentions the use of a nitrocellulose filter-binding assay, which suggests that the authors are measuring the activity of the purified enzyme in relation to its binding to DNA, a common approach in enzymology studies.\n",
        "doc_id": "fc26e145-c3ea-4bdc-b303-88b4d6846eb3"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the Dnmt3b2 protein and includes a detailed description of a methyl transfer activity assay, which is an in vitro enzymatic assay used to measure the activity of the purified enzyme. The methods section outlines the preparation of the reaction mixture, the conditions under which the enzymatic reaction occurs, and how the results are analyzed, all of which are characteristic of experimental enzymology studies.\n",
        "doc_id": "688b63bd-69f2-49fd-b097-473d0eca5da6"
      }
    ]
  },
  "21069965": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/21069965.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the in vitro reconstitution and verification of the activity of the polyketide synthase LovF, including the use of 13C-labeled malonyl-CoA to form intermediates and the detection of these intermediates using mass spectrometry. The paper describes the enzymatic processes involved in the biosynthesis of R-methylbutyrate, detailing how the enzyme interacts with substrates and the formation of intermediates, which are key aspects of experimental enzymology. The methods employed, such as the phosphopantetheine ejection assay, indicate a focus on measuring enzyme activity and characterizing enzymatic reactions, which aligns with the definition of experimental enzymology.\n",
        "doc_id": "791ae0ae-9474-43dd-950e-2526d8735486"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text describes the cloning, expression, and purification of the enzyme holo-LovF, which is a key aspect of experimental enzymology. It also details the in vitro reactions and assays conducted to analyze the enzyme's activity, including the incubation of holo-LovF with malonyl-CoA and the subsequent mass spectrometric analysis of the resulting intermediates. The methods section outlines the purification and characterization of the enzyme, which are essential components of experimental enzymology studies.\n",
        "doc_id": "86fac109-b1b6-427e-8948-5713835e7a3d"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the incubation of holo-LovF with a substrate (malonyl-CoA) and the subsequent analysis of the resulting peptides through limited proteolysis and HPLC. This indicates that there is an enzymatic assay being performed to measure the activity of the enzyme (holo-LovF) in the presence of a substrate. The mention of active site-containing peptides and the use of techniques like HPLC and FT-ICR-MS to analyze the enzyme's activity further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "181d5601-5d0c-4b16-85be-49f8d304fcf0"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the incubation of holo-LovF with malonyl-CoA to monitor the formation of acyl intermediates, which indicates an in vitro enzymatic assay. The paper details the methods used to analyze the resulting peptides through mass spectrometry, including the detection of specific ions that correspond to enzymatic activity. The focus on the formation of malonyl-S-ACP and acetyl-S-ACP, as well as the experimental conditions tested (such as varying concentrations of malonyl-CoA), further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "017bfd73-b857-4844-a123-a32fe522a095"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the incubation of holo-LovF with malonyl-CoA and the detection of various intermediates and products through mass spectrometry, indicating that in vitro enzymatic assays were performed to measure the activity of the enzyme. The paper mentions specific concentrations of malonyl-CoA used in the reactions, the detection of malonyl-S-LovF, and the use of labeled substrates, all of which are characteristic of experimental enzymology studies that focus on enzyme activity and kinetics.\n",
        "doc_id": "14a9ff16-f052-41c9-95d1-d1f70766aa1e"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme LovF, as well as in vitro assays to measure its activity. The text mentions incubating holo-LovF with various substrates (like malonyl-CoA and acetoacetyl-CoA) and analyzing the products formed using mass spectrometry (FT-ICR-MS). This indicates that the authors are conducting enzymatic assays to evaluate the function of LovF and its ability to catalyze the formation of specific biosynthetic intermediates, which is a hallmark of experimental enzymology.\n",
        "doc_id": "81e176d2-8b4d-4395-b953-bbbf800f5da7"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme holo-LovF, and it details in vitro enzymatic assays that measure the activity of the purified enzyme. The paper describes various incubation conditions and the detection of enzymatic products using techniques like FT-ICR-MS, which are indicative of enzymatic activity and the formation of intermediates in the enzymatic reactions being studied. The focus on the reaction mechanisms and the specific conditions under which the enzyme operates further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "061747a7-2c6a-4064-aa07-b5a2d82b98e1"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the co-incubation of holo-LovF with substrates such as acetoacetyl-CoA and SAM, followed by the addition of NADPH to measure the formation of specific intermediates. This indicates that there are in vitro enzymatic assays being performed to assess the activity of the enzyme holo-LovF, which is a key characteristic of experimental enzymology. The mention of reaction conditions, the detection of intermediates, and the use of mass spectrometry to analyze the products further supports this classification.\n",
        "doc_id": "d9835e09-d217-4b20-86ca-0e6b203bda28"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme LovF, as well as in vitro enzymatic assays to measure the activity of the purified enzyme. The text describes various experimental conditions, such as the incubation of holo-LovF with malonyl-CoA and the generation of acyl intermediates, which are key components of enzymatic assays. Additionally, the paper details the monitoring of active site occupancy and the formation of specific intermediates, indicating a focus on the enzymatic activity and mechanisms involved in the biosynthesis of R-methylbutyrate.\n",
        "doc_id": "d0f411c3-164d-484e-b010-0e2c61f45b62"
      }
    ]
  },
  "19710136": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/19710136.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the VSV L protein and P protein, as well as the in vitro enzymatic assays used to measure the methylation activities of the purified enzyme. The methods section details the purification process using Ni-nitrilotriacetic acid–agarose and ion-exchange chromatography, and it describes the conditions under which the methylation reactions were performed, including the use of S-adenosyl-L-methionine (SAM) as a methyl donor. The paper also outlines the experimental setup for assessing the enzymatic activity, indicating a clear focus on enzymology.\n",
        "doc_id": "ca2ea6d6-b9d4-44ae-99ae-df9274d1c4bf"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the VSV L protein, which possesses mRNA cap methyltransferase (MTase) activities. The paper details in vitro assays to measure the enzymatic activity of the purified L protein, specifically focusing on the kinetics of ribose 2'-O and G-N-7 methylation of RNA. The methods include monitoring cap methylation over time and analyzing the products of the reactions using techniques such as TLC and PhosphorImager, which are typical in experimental enzymology studies. The results demonstrate the enzyme's activity and the order of methylation, which are key aspects of enzymatic assays.\n",
        "doc_id": "d43579b8-420a-47ae-a6de-f2c70bd16153"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a protein/enzyme (the vaccinia virus capping enzyme) and describes in vitro enzymatic assays to measure the activity of the purified enzyme, specifically focusing on the kinetics of cap methylation. The methods section details the incubation of RNA substrates with the enzyme in the presence of S-adenosylmethionine (SAM) and the subsequent analysis of methylation products using techniques like TLC and quantification with a PhosphorImager. This indicates a clear focus on enzymatic activity and the biochemical properties of the enzyme, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "1973704e-0bb5-4730-87ea-14d97e71f008"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activities of the VSV L protein, specifically focusing on the methylation of RNA substrates. The paper describes the experimental setup where RNA substrates are incubated with the VSV L protein in a methylation buffer, and the resulting products are analyzed using techniques such as TLC and PhosphorImager visualization. The mention of specific enzymatic activities, the conditions under which the reactions occur, and the analysis of the effects of amino acid substitutions on these activities all point to a detailed investigation of enzymatic function, which is characteristic of experimental enzymology.\n",
        "doc_id": "f7a18954-9633-4300-8cbf-401b4920e25d"
      }
    ]
  },
  "25859931": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/25859931.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzymes PenG and PenI from Escherichia coli, which is a key aspect of experimental enzymology. The paper also describes in vitro biochemical assays to measure the activity of these enzymes with specific substrates, including the incubation of compound 2 with GPP and DMAPP to assess the enzymatic activity. The results of these assays are presented, indicating the conversion of substrates and the identification of products, which are essential components of experimental enzymology studies.\n",
        "doc_id": "555a8330-6e87-4a4a-bd3c-e4bb95947c41"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro enzymatic assay involving the enzyme PenG, where the substrate 9 is incubated with PenG, DMAPP, and MgCl2, followed by LC−MS analysis to measure the conversion of 9 to other compounds. The paper details the experimental setup and results of these assays, confirming the enzymatic activity of PenG in the prenyl elongation reaction. Additionally, it mentions the use of a ΔpenG mutant to identify substrates and the characterization of reaction products, which are typical elements found in experimental enzymology studies.\n",
        "doc_id": "ebf9780b-c374-42fe-b6e9-fc71b08bd948"
      }
    ]
  },
  "15705854": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/15705854.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the overexpression and purification of the HEN1 protein fused to glutathione S-transferase (GST) in Escherichia coli, followed by an in vitro methylation assay to measure the activity of the purified enzyme on various RNA substrates. The paper details the experimental setup, including the use of 14C-labeled SAM and the results of the methylation reactions, which confirm HEN1's activity as a methyltransferase. This focus on enzyme activity and the specific assays conducted aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "afb89d76-fd44-48f1-9af7-14cf5d3eb563"
      }
    ]
  },
  "31346037": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31346037.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methyltransferase assay performed to determine whether Hspa8 is methylated by Mettl21c, which involves the use of recombinant proteins and the measurement of methyl group incorporation. This indicates that the paper includes an enzymatic assay to measure the activity of the purified enzyme, aligning with the characteristics of experimental enzymology. Additionally, the paper mentions the overexpression and purification of Mettl21c, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "785cf5f2-14f4-48d2-94e8-8732c38e51e7"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the in vitro methyltransferase activity of the enzyme Mettl21c on substrates Vcp and Hspa8, including specific details about the assay conditions (e.g., constant concentration of Mettl21c and varying concentrations of substrates) and the measurement of methyl groups transferred, which indicates enzymatic activity. The paper also provides kinetic parameters such as Km values for the interactions, which are typical in enzymology studies. Additionally, it describes the purification and characterization of the enzyme and its substrates, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "da84697c-8647-4e0b-85c2-8a0b1757552e"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methyltransferase activity of Mettl21c, which is a key aspect of experimental enzymology. The methods section mentions the use of a substrate (K561A-Hspa8 or WT Hspa8) and the presence of [¹⁴C]SAM, indicating that an enzymatic assay was performed to measure the activity of the enzyme. Additionally, the paper provides data on the effect of varying concentrations of Mettl21c on the methylation of Hspa8, which is a typical approach in experimental enzymology to assess enzyme kinetics and activity.\n",
        "doc_id": "cb1dc42b-789a-4b3c-9152-5a11efed93f8"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins, specifically mentioning the use of plasmids to produce His₆-tagged proteins in E. coli, which is a common method in enzymology for obtaining purified enzymes. Additionally, the paper describes the use of mass spectrometry to analyze peptides, which implies that enzymatic activity or modifications (such as methylation) are being studied. The detailed methods for protein preparation, purification, and analysis indicate a focus on enzymatic assays and protein functionality, characteristic of experimental enzymology research.\n",
        "doc_id": "dfbf41f4-366e-4445-8848-ee251604660c"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the methodology for performing in vitro methyltransferase reactions, which includes details about the reaction conditions, the components used (such as the methyltransferase enzyme, substrates, and reaction buffer), and the process for stopping the reactions and measuring the results (e.g., using scintillation counting to measure radioactivity). The mention of the purification of proteins using nickel-nitrilotriacetic acid resin and the subsequent assays to measure enzyme activity are key indicators of experimental enzymology.\n",
        "doc_id": "d104b056-1ecb-46bf-ade1-d1e8aa412803"
      }
    ]
  },
  "15254179": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/15254179.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the isolation and purification of the C protein, which is a crucial step in experimental enzymology. The paper details the methods used for the purification of the protein, including size exclusion chromatography and the use of detergents, which are common practices in enzymology studies. Additionally, it mentions the in vitro assembly of capsid-like structures using the purified C protein and nucleic acids, indicating that the enzymatic activity of the protein is being assessed in a controlled environment. The focus on protein purification and subsequent assays aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "5a3ed8fb-cb96-4908-8d98-ed5b2500ee86"
      }
    ]
  },
  "18022563": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/18022563.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the kinetic analysis of human PPT (phosphopantetheine transferase), detailing the effects of site-directed mutagenesis on enzyme activity, which is a key aspect of experimental enzymology. The paper includes specific mentions of kinetic parameters such as Km and kcat, which are essential for understanding enzyme activity. Additionally, it describes the role of specific amino acid residues in binding and catalysis, indicating that in vitro enzymatic assays were performed to measure the activity of the enzyme under various conditions. The focus on the catalytic mechanism and the structural data supporting the enzymatic function further solidifies its classification as an experimental enzymology paper.\n",
        "doc_id": "9366c483-1a48-4d84-b309-abd12cb8ccb4"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the kinetic properties of human PPT (phosphopantetheine transferase) and includes detailed measurements of kinetic parameters such as Kₘ and kcat for various active-site mutants. The paper also describes the loss of activity in specific mutant proteins, indicating that in vitro enzymatic assays were performed to assess the activity of the purified enzyme. The mention of the role of specific amino acids in catalysis and the comparison of mechanisms between different types of PPTs further supports the experimental enzymology focus of the study.\n",
        "doc_id": "1a655f45-bb03-47aa-9aad-6161889304ab"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the cloning, expression, and purification of the human PPT (phosphopantetheine transferase) enzyme, detailing the methods used to achieve high-level soluble protein production in E. coli, including IPTG induction and various purification steps such as immobilized metal affinity chromatography and gel filtration. Additionally, it mentions the use of the purified enzyme for activity measurements, which indicates that enzymatic assays are part of the study. The focus on the enzyme's structure and function, along with the experimental procedures for its preparation, aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "119f4f0e-de99-4f6b-b799-7f74458ba59b"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of a protein/enzyme (PPT) using methods such as NiNTA column purification and anion exchange chromatography. Additionally, it includes a detailed description of an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically mentioning the conditions under which the mutant PPT activities were assayed, the use of [1-14C]acetyl-CoA as a substrate, and the methods for quantifying the enzymatic activity. This focus on enzyme purification and activity measurement aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "1b853852-a696-426a-ae06-9a91236cd373"
      }
    ]
  },
  "23285036": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/23285036.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. The authors discuss the expression and activity of calmodulin-lysine N-methyltransferase (CaM KMT), which is a methyltransferase enzyme. They mention that CaM KMT catalyzes the formation of a trimethyllysyl residue at position 115 in calmodulin, indicating that they are studying the enzymatic activity of this protein. Additionally, the paper includes details about the expression of the enzyme at the transcript and protein levels, as well as its interaction with Hsp90, which suggests a focus on the functional aspects of the enzyme. The mention of enzymatic activity and the characterization of the enzyme's role in methylation aligns with the criteria for an experimental enzymology paper.\n",
        "doc_id": "df19863c-66ad-4c12-82a2-e5df57c6a3c3"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme CaM KMT (calmodulin-lysine N-methyltransferase) using a SUMO vector, and it describes an in vitro enzymatic assay to measure the activity of the purified enzyme. The methods section details the preparation of cell lysates, the components of the assay, and the conditions under which the enzymatic reactions were performed, including the use of [³H-methyl] AdoMet as a methyl donor. Additionally, the results section provides evidence of the enzyme's activity through the detection of methylation on calmodulin, confirming the enzymatic function of the purified CaM KMT.\n",
        "doc_id": "9ea0535b-6822-48d4-a356-3b1b5ee1fed1"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the CaM KMT protein, as indicated by the mention of \"incubation of GST-CaM KMT fusion protein purified from bacteria with [³H-methyl] AdoMet,\" which suggests an enzymatic assay to measure the activity of the purified enzyme. The paper also describes the use of a specific substrate (AdoMet) for the enzyme, which is a key aspect of experimental enzymology. Additionally, the methods for determining the subcellular localization of the enzyme and the expression patterns further support the focus on the enzyme's functional characterization.\n",
        "doc_id": "3abdb60c-7e1b-44ef-8c1c-1a73828be894"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro automethylation of the CaM KMT protein, which involves incubating the protein with a methyl donor (AdoMet) and measuring the resulting activity through SDS-PAGE and fluorography. The methods section indicates the purification of the enzyme and the enzymatic assay used to assess its activity, which are key components of experimental enzymology.",
        "doc_id": "bcee16f4-4e44-4e07-bea5-6f7b3670d9e3"
      }
    ]
  },
  "27578809": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/27578809.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Zika virus NS1 protein, detailing the methods used for gene cloning, expression in baculovirus, and purification techniques such as metal affinity chromatography and ion-exchange chromatography. The paper also mentions the use of crystallization and X-ray diffraction data collection, which are common in structural biology studies related to enzymology. Although it primarily focuses on the structural aspects of the NS1 protein, the methods section indicates a clear involvement in the purification and preparation of a protein that could be further analyzed for enzymatic activity, which aligns with the characteristics of experimental enzymology.\n",
        "doc_id": "0295ad80-663c-414f-946c-4f0b53b04fa0"
      }
    ]
  },
  "30830907": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/30830907.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the NS2B3 protease from dengue virus, as indicated by the mention of cloning and expressing the protease in a recombinant GST prokaryotic expression system. Additionally, it includes an enzymatic assay that measures the substrate cleavage efficiency of the NS2B3 protease, which is a key aspect of experimental enzymology. The paper focuses on the functional analysis of the enzyme and its variants, which aligns with the typical content found in experimental enzymology studies.\n",
        "doc_id": "da5333ec-bc03-436b-a935-adebbef40e99"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the enzymatic activity of the DENV1B NS2B3-K55R protein and compares it to the wild type NS2B3, indicating that an enzymatic assay was performed to measure the activity of the purified enzyme. The mention of \"lower enzymatic activity\" and \"higher cleavage activity\" in relation to specific mutations suggests that the authors conducted in vitro assays to evaluate the enzymatic properties of the proteins involved. This aligns with the characteristics of experimental enzymology papers, which typically include the overexpression, purification, and activity measurement of enzymes.\n",
        "doc_id": "ef8e80ba-4a03-4f80-a893-7d48d272867e"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the overexpression and purification of the NS2B3 protease from dengue viruses, which is a key aspect of experimental enzymology. It also describes the enzymatic activity of the purified NS2B3 protease using a specific substrate (NS2B3-pNA), measuring the cleavage efficiency over time, which indicates that in vitro enzymatic assays were performed to assess the activity of the enzyme. The mention of different concentrations of the enzyme and the statistical analysis of the results further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "4a47b2c1-a57d-453b-9fcb-4f6a995e0f7a"
      },
      {
        "page": 13,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the NS2B3 protease from dengue virus, detailing the use of a bacterial expression system and purification methods such as GST affinity chromatography. Furthermore, it includes an in vitro enzymatic assay where the activity of the purified NS2B3 enzyme is measured by incubating it with a specific substrate and analyzing the cleavage efficiency, which is a key characteristic of experimental enzymology papers.\n",
        "doc_id": "f8b5cc3b-a94a-42b0-b614-0b726b4b2c1d"
      }
    ]
  },
  "21558554": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/21558554.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the purification and activity of a protein (PP2A) and its interaction with a substrate (BRI1) in vitro. Specifically, it mentions the use of a purified mammalian PP2A to dephosphorylate the BRI1 kinase domain, indicating that an enzymatic assay was performed to measure the activity of the enzyme. The results of this assay are described, including the detection of a faster-moving band in SDS-PAGE, which suggests that the enzyme successfully dephosphorylated its substrate. This aligns with the characteristics of an experimental enzymology paper, as it involves the purification of an enzyme and the measurement of its activity through an in vitro assay.\n",
        "doc_id": "b0abbd4b-dcc0-4a94-8dc6-9c52d73a07c0"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro dephosphorylation of the kinase domain of BRI1 by PP2A, which indicates an enzymatic assay to measure the activity of the purified enzyme. The paper mentions the use of Western blotting to detect the phosphorylation status of BRI1, and it describes the experimental setup involving the interaction between PP2A and BRI1, which is characteristic of experimental enzymology studies. Additionally, the paper provides details about the effects of PP2A on BRI1 signaling, further emphasizing the enzymatic activity being investigated.\n",
        "doc_id": "4c46248a-29ae-487b-a029-f770ec8cdeb0"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of recombinant proteins (GST-SBI1 and GST-sbi1) and their use in in vitro methylation assays, which are key components of experimental enzymology. The methods section describes the purification process, the enzymatic reactions involving these proteins, and the subsequent analysis of the results through techniques like SDS-PAGE and Western blotting. The focus on measuring the activity of the purified enzymes through these assays aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "c827221e-7011-4065-941f-3682aeb5bf54"
      }
    ]
  },
  "21884704": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/21884704.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the structure and function of the MycE enzyme, including details about its active site architecture and the coordination of metal ions, which are critical for its enzymatic activity. The paper mentions the introduction of substrates into crystals and the observation of electron density maps, indicating that in vitro assays were likely performed to study the enzyme's activity. Additionally, the paper describes the interactions between the enzyme and its substrates, which are essential components of enzymatic assays. Overall, the focus on the enzyme's structure, substrate binding, and metal dependence aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "480157b8-3de6-4e3c-8f81-02ab8c52e5f2"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the activity of the MycE enzyme and includes details about testing the proposed mechanism through single-residue substitutions of specific amino acids (His278 and Tyr208) to assess their impact on enzymatic activity. The paper mentions that these substitutions were made to evaluate the role of these residues in the enzyme's function, which is a key aspect of experimental enzymology. Additionally, it provides results indicating the lack of activity for certain substitutions, which is indicative of an in vitro enzymatic assay to measure the activity of the purified enzyme.\n",
        "doc_id": "b13285b7-3718-4156-96d7-d7963d923387"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the structure and function of the MycE enzyme, including details about its active site and the effects of specific mutations on enzyme activity, as indicated by the table of measured activity for MycE mutants. The mention of \"measured activity\" and the specific activity percentages for different MycE variants suggest that in vitro enzymatic assays were performed to assess the functionality of the enzyme, which is a key characteristic of experimental enzymology papers.\n",
        "doc_id": "ab2dca82-1084-466b-9edb-9c039384e382"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the MycE protein, detailing the methods used for protein production, including the use of a His-tag and Ni-NTA affinity chromatography for purification. Additionally, the paper mentions the crystallization of the MycE protein in the presence of substrates (SAM and SAH), which indicates that the authors are investigating the enzyme's structure and potentially its activity. The focus on the enzyme's substrate specificity and the implications for biosynthetic engineering further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "7f511f84-0480-4edc-88d3-93a9d3caf7d8"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the MycE enzyme, as indicated by the mention of using the pET-28b-mycE expression plasmid and transforming E. coli for overexpression. Additionally, it details the enzymatic assays performed to measure the activity of the purified enzyme, including specific conditions for the assay (e.g., enzyme concentration, substrate concentration, and incubation conditions). The paper also describes the procedures for these assays, which is a hallmark of experimental enzymology studies.\n",
        "doc_id": "7c6c90a9-6cb6-40b0-9767-ef750c597eea"
      }
    ]
  },
  "8189517": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/8189517.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an experimental enzymology paper. It discusses the development of a cell-free trans cleavage assay for the yellow fever virus NS2B-3 proteinase, which is a clear indication of an in vitro enzymatic assay to measure the activity of the purified enzyme. The paper details the use of a substrate to demonstrate NS2B-3 proteinase-mediated cleavage, and it mentions the requirement of specific proteins for this cleavage, which aligns with the typical structure of experimental enzymology papers that focus on enzyme activity and characterization.\n",
        "doc_id": "8d747721-3cef-41a2-8e70-48755f50f705"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins/enzyme, specifically mentioning the use of various plasmids and viral recombinants to express YF (Yellow Fever) proteins. The paper includes details about in vitro assays, such as the \"YF 2B-3 proteinase assay,\" where the activity of the proteinase is measured using radiolabeled substrates and various conditions. The methods section describes the preparation of cell extracts, the use of immunoprecipitation, and the analysis of proteinase activity, all of which are characteristic of experimental enzymology studies.\n",
        "doc_id": "93bfcd46-8a7c-483a-ac70-0a8ede388a71"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the development of an in vitro trans-cleavage assay for the YF NS2B-3 proteinase, which involves the overexpression and purification of the enzyme, as well as the measurement of its proteolytic activity. The text mentions the use of various methods such as SDS-PAGE for analyzing the cleavage products and describes the conditions under which the enzymatic activity was assessed, indicating a focus on enzymatic assays. Additionally, it details the preparation of lysates from YF-infected cells and the testing of different detergents as solubilizing agents, which are common practices in experimental enzymology.\n",
        "doc_id": "66cd6872-1d37-4d8d-85bc-f649cac292ce"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the performance of proteinase assays, specifically detailing the use of cell lysates from YF-infected cells and the incubation of substrates with these lysates to measure proteolytic activity. The paper mentions the purification of proteins, the conditions under which the assays were conducted (such as temperature and substrate concentration), and the results of these assays, which are characteristic of experimental enzymology studies. The focus on enzymatic activity and the methods used to assess it clearly align with the criteria for an experimental enzymology paper.\n",
        "doc_id": "f59a66df-1790-47fb-bd0a-93fbb7f45a22"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of the NS2B-3 proteinase, including the use of in vitro assays to demonstrate its cleavage activity on specific substrates. The text mentions the use of constructs for expressing the protein, the results of in vitro transcription-translation experiments, and the identification of cleavage sites, which are all indicative of experimental enzymology. The paper also describes the enzymatic activity of the proteinase and its role in processing viral proteins, which aligns with the typical focus of experimental enzymology studies.\n",
        "doc_id": "c2c2042b-2432-49fe-924e-816a4049d97d"
      }
    ]
  },
  "29163603": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/29163603.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of fibrillarin, specifically highlighting a novel ribonuclease activity associated with the AtFib2 variant of fibrillarin. The paper mentions the differences in enzymatic activity between AtFib1 and AtFib2, indicating that the authors likely conducted in vitro assays to measure this activity. Additionally, the focus on the ribonuclease activity and its implications for rRNA processing suggests that the authors performed experiments to characterize the enzymatic function of the purified protein, which is a hallmark of experimental enzymology.\n",
        "doc_id": "3e7f6036-58ad-447f-aa13-3cf61f3a1302"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and characterization of fibrillarin proteins from Arabidopsis thaliana, specifically mentioning the discovery of ribonuclease activity associated with these proteins. The Methods section outlines the cloning of the fibrillarin genes and the use of specific primers for amplification, which indicates a focus on the overexpression and purification of the enzyme. Additionally, the paper implies that there are enzymatic assays involved in distinguishing the activity between the two fibrillarins, which is a key aspect of experimental enzymology.\n",
        "doc_id": "98ef0fbe-ce10-4fcb-9872-94b378fef8f3"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of Arabidopsis thaliana fibrillarins in E. coli, detailing the methods used for protein extraction and purification, including the use of Ni-NTA agarose and Q sepharose chromatography. Additionally, it describes an in vitro ribonuclease assay to measure the activity of the purified fibrillarins, which is a key component of experimental enzymology. The paper includes specific details about the conditions and buffers used for the enzymatic assays, indicating a focus on enzyme activity measurement.\n",
        "doc_id": "7651bef3-397b-48ef-8aff-55a7f30adcf8"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text mentions the purification of fibrillarin proteins from Arabidopsis thaliana and describes an in-gel ribonuclease activity assay to measure the enzymatic activity of the purified fibrillarin. This indicates that the authors are investigating the functional properties of the enzyme, which is a key aspect of experimental enzymology. Additionally, the paper discusses the expression levels and structural differences of the fibrillarin proteins, which are relevant to understanding their enzymatic functions.\n",
        "doc_id": "d9bfa888-8a42-4f46-b451-3a731cc52053"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of two fibrillarin proteins (AtFib1 and AtFib2) and their ribonuclease activity, which is measured through in vitro assays. The authors describe the purification process and the subsequent enzymatic assays that demonstrate the ribonuclease activity of the proteins, including their susceptibility to degradation and activation by calcium. The paper provides detailed results from these assays, indicating the enzymatic activity of the purified proteins, which is a hallmark of experimental enzymology.\n",
        "doc_id": "7a2eafaf-5cb4-435e-9d46-f46bb05fbbac"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the AtGAR2 domain of fibrillarin and its ribonuclease activity, which is measured through in-gel activity assays and under native conditions. The paper provides details on the enzymatic activity of the purified protein, specifically how it interacts with RNA substrates and the effects of phosphatidic acid on its activity. This focus on the purification and functional characterization of an enzyme aligns well with the criteria for experimental enzymology papers.\n",
        "doc_id": "78136c9c-26c6-4d42-b338-79dc7fb2e176"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the ribonuclease activity of specific protein domains (AtGAR2 and Atα2) and includes details about in-gel ribonuclease activity assays, which measure the enzymatic activity of these proteins. The paper mentions the degradation of RNA by AtGAR2, indicating that the authors performed an in vitro enzymatic assay to assess the activity of the purified enzyme domains. Additionally, the results show a direct relationship between the amount of AtGAR2 added and the degradation of rRNA, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "d4c63f33-f4e5-4b50-91ca-ce162d39c4da"
      }
    ]
  },
  "12403464": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/12403464.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the identification and characterization of two proteins, Trm8 and Trm82, that are required for the 7-methylguanosine modification of tRNA. The paper mentions the purification of these proteins and their coexpression, which is necessary for the methyltransferase activity. Additionally, it provides evidence that extracts from strains lacking either gene have undetectable m⁷G methyltransferase activity, indicating that the enzymatic activity is being measured. The focus on the enzymatic assay and the purification of the proteins aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "a2d43c5e-bcaf-4fc5-abaa-230ea44623ad"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the detection of tRNA m⁷G methyltransferase activity in yeast extracts, which involves an in vitro enzymatic assay using S-adenosylmethionine (SAM) as a methyl group donor and labeled pre-tRNA as the substrate. The paper describes the methodology for the assay, including the use of thin layer chromatography (TLC) to separate and identify the modified nucleotides formed during the reaction. This focus on enzyme activity measurement and the purification of the enzyme aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "ee8fcfae-d400-4d0a-a7f2-7e12381c25f2"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the detection of m⁷G methyltransferase activity in yeast extracts and describes the use of a specific assay involving [a-³²P]-GTP labeled pre-tRNAᴾʰᵉ and SAM to measure the enzymatic activity. The paper details the incubation of yeast extracts and the subsequent analysis of modified nucleotides using two-dimensional TLC, which is a common method in experimental enzymology to assess enzyme activity. Additionally, it mentions the purification of GST-ORF fusion proteins and the screening of these proteins for methyltransferase activity, further indicating a focus on enzymatic assays and protein characterization.\n",
        "doc_id": "f78db441-61a0-4e62-a9fe-8f4c65d35ace"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins Trm8 and Trm82, which are implicated in m⁷G methyltransferase activity. The paper details the experimental approach used to analyze the enzymatic activity of these proteins, including the observation that strains lacking either protein show no detectable tRNA m⁷G methyltransferase activity. Additionally, it describes the methods used to quantify the m⁷G content in tRNA, indicating that the authors performed in vitro assays to measure the activity of the purified enzyme. This focus on enzymatic assays and the characterization of enzyme activity aligns well with the criteria for experimental enzymology papers.\n",
        "doc_id": "35f712ae-f9fa-4626-80d3-ff4a34630aaf"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Trm8 and Trm82 proteins, which are involved in m⁷G methyltransferase activity. The paper details the methods used to express these proteins in E. coli, their purification, and the subsequent in vitro assays that measure their enzymatic activity on pre-tRNA. Specifically, it mentions the assay for m⁷G methyltransferase activity and the results of these assays, indicating that the purified proteins modify G46 of pre-tRNA to m⁷G. This focus on protein purification and enzymatic assays is characteristic of experimental enzymology.\n",
        "doc_id": "be91ddd0-abae-4e97-b321-553639878e6e"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and functional testing of human orthologs of yeast proteins involved in tRNA modification, specifically focusing on the m⁷G methyltransferase activity. The paper mentions the expression of METTL1 and WDR4 proteins in yeast and the subsequent assays conducted to measure the restoration of methyltransferase activity in yeast extracts, which is a key aspect of experimental enzymology. The mention of \"assaying extracts for activity\" and the results indicating the restoration of enzymatic function further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "b5e41720-97b1-4825-973b-662fc1680227"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of Trm8 and Trm82 proteins from E. coli, which is a key aspect of experimental enzymology. The paper also details the enzymatic assay performed to measure the m⁷G methyltransferase activity of these purified proteins, including the use of pre-tRNA as a substrate and S-adenosyl-methionine as a donor. The results of the enzymatic assays, including the analysis of the reaction products and the effects of co-purification on enzyme activity, further support its classification as an experimental enzymology paper.\n",
        "doc_id": "b4aee6a1-8ce7-4837-8f18-41a015c66939"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Trm8 and Trm82 proteins, which are involved in the methyltransferase activity related to tRNA modification. The paper provides evidence of the enzymatic activity of the Trm8/Trm82 complex, including details about the conditions under which the methyltransferase activity is observed and the methods used to analyze the activity, such as the treatment of pre-tRNA with SAM and subsequent analysis on a polyacrylamide gel. This indicates that the authors conducted in vitro enzymatic assays to measure the activity of the purified enzyme, which is a hallmark of experimental enzymology.\n",
        "doc_id": "d8a68a26-e379-4fac-8385-9b14f065885f"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the assay for m⁷G methyltransferase activity, detailing the preparation of substrates and the specific conditions under which the enzymatic reactions are carried out. The Methods section includes a description of the reaction mixtures, incubation conditions, and the subsequent analysis of the products, which are all indicative of an in vitro enzymatic assay to measure the activity of the purified enzyme. Additionally, the paper mentions the purification of proteins and their use in the enzymatic assays, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "c49e569f-5e77-4db4-b7c7-73f428e20ab9"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the identification of human orthologs responsible for m⁷G modification of tRNA and describes the assay for m⁷G methyltransferase activity, which is a key aspect of enzymology. The paper mentions the use of yeast extracts and the incubation of pre-tRNA with Trm8/Trm82 proteins, indicating that an in vitro enzymatic assay was performed to measure the activity of the methyltransferase. Additionally, the methods section outlines the expression and purification of proteins, which is typical in experimental enzymology studies.\n",
        "doc_id": "7ee02b71-e549-4b70-a54e-e8411a2d5d42"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins (specifically, fusion proteins like His6-maltose-binding protein-ORF and GST-ORF fusion proteins) and describes methods for their purification using techniques such as IgG-sepharose chromatography and TALON cobalt-affinity resin. Additionally, the paper mentions the preparation of crude extracts from E. coli and yeast, which is a common step in enzymology studies. Although the specific enzymatic assays are not detailed in the provided text, the context indicates that the paper is focused on the experimental aspects of protein/enzyme handling, which is characteristic of experimental enzymology.\n",
        "doc_id": "77439f3e-51d6-4733-8980-aecb59ce2217"
      }
    ]
  },
  "16768442": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/16768442.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the enzyme tRNA(m1G37) methyl transferase and details the identification of critical residues for catalysis, specifically focusing on the proline at position 267. The paper mentions steady-state kinetic analysis and single turnover kinetic analysis to measure the enzyme's activity, which indicates that in vitro enzymatic assays were performed to assess the effects of mutations on the enzyme's catalytic potential and substrate-binding capabilities. This aligns with the characteristics of experimental enzymology, as it involves the overexpression, purification, and activity measurement of an enzyme.\n",
        "doc_id": "d4266bc7-b6d0-4fc1-9af8-798d75e14c74"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme Trm5 from Methanocaldococcus jannaschii, as indicated in the \"Enzyme Purification and Mutagenesis\" section. The paper also details the methods used for enzyme kinetic assays, including conditions for the methylation assay and the use of steady-state and transient-state kinetics to assess the enzyme's catalytic activity. These elements clearly demonstrate the experimental approach typical of enzymology studies, focusing on the activity and characteristics of a specific enzyme.\n",
        "doc_id": "d76fc026-e0b6-4e91-9f77-82b7d98f9063"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the M. jannaschii Trm5 enzyme, as well as the use of various assays to measure its enzymatic activity, including a tRNA methyl transferase activity assay using [³H]‑AdoMet as a cofactor. The paper details the methods for purifying the enzyme, the conditions under which the enzymatic assays were performed, and the analysis of the activity of various mutants, which is characteristic of experimental enzymology studies.\n",
        "doc_id": "3db59ca4-3573-4ee3-a279-c8ac9cd33871"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Trm5 enzyme from M. jannaschii, and it includes detailed kinetic analyses of both the wild-type enzyme and various mutants. The paper provides specific kinetic parameters (kcat and Kₘ) derived from in vitro enzymatic assays that measure the activity of the purified enzyme with respect to tRNA and AdoMet substrates. The methodology includes steady-state kinetic analysis, time course measurements, and the use of the Michaelis-Menten equation to interpret the data, which are all hallmarks of experimental enzymology studies.\n",
        "doc_id": "bc49f009-05b8-4391-a95d-a2f446497c39"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Trm5 enzyme, as well as various assays to measure its activity and binding affinity for substrates like tRNA and AdoMet. The paper details the use of gel shift assays to determine the equilibrium dissociation constant (Kd) for tRNA binding and fluorescence titration assays to measure the binding affinity for AdoMet, which are both key components of experimental enzymology. Additionally, it mentions the use of UV cross-linking assays to confirm binding interactions, further emphasizing the experimental approach to studying enzyme activity.\n",
        "doc_id": "da8f8a48-5c7b-4d43-8296-22f93d21d845"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Trm5 enzyme and its mutants, as well as detailed kinetic analyses of their enzymatic activities. The paper includes specific mentions of steady-state kinetic analysis, single turnover kinetics, and the measurement of catalytic rates (kcat/Kₘ and kchem), which are all indicative of in vitro enzymatic assays to assess enzyme activity. Additionally, the use of SDS-PAGE for analyzing enzyme purity and the effects of mutations on enzyme function further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "3fd8c6ab-177f-4af0-abde-9136e43a4697"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a protein/enzyme, specifically the Trm5 enzyme, and includes detailed in vitro enzymatic assays to measure the activity of the purified enzyme. The paper presents data on single turnover kinetics, comparing the kchem values of wild-type and mutant enzymes, and discusses the effects of specific mutations on enzyme activity and substrate binding. The mention of kinetic parameters such as kcat and Km, as well as the experimental setup for measuring enzyme activity, clearly indicates that this is an experimental enzymology study.\n",
        "doc_id": "9bbda003-d42e-41b6-9338-464096dadf40"
      }
    ]
  },
  "19101564": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/19101564.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the establishment of an in vitro fluorescence polarization assay to measure GTP binding to the purified MTase protein, which is a key aspect of experimental enzymology. The paper details the binding affinity measurements (Kd values) for GTP and its analogs, as well as the effects of specific mutations on binding, indicating a focus on the enzymatic activity and interactions of the enzyme. Additionally, the mention of purification and characterization of the MTase protein aligns with the typical methods used in experimental enzymology studies.\n",
        "doc_id": "fbb32894-8f90-404e-b671-b777e7516b4d"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the binding affinity of various guanosine triphosphate (GTP) analogs to a methyltransferase (MTase) enzyme, including detailed measurements of dissociation constants (Kd) and inhibition constants (Ki) for different mutants and analogs. The paper mentions the expression and purification of mutant proteins, as well as the use of binding assays to assess the interaction of these proteins with GTP and its analogs, which are key components of experimental enzymology. The focus on the enzymatic activity and binding characteristics of the purified enzyme indicates that this research is centered around experimental enzymology.\n",
        "doc_id": "b5d479a5-e854-4cb1-a48f-91f91a65bfd5"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the production and purification of recombinant flavivirus MTase proteins, detailing the methods used for overexpression in E. coli, lysis, and purification through various chromatography techniques. Additionally, it mentions the use of purified proteins for biochemical studies, which implies that enzymatic assays may be conducted to measure the activity of the purified enzyme, although specific assay details are not provided in the excerpt. The focus on the binding interactions and structural analysis of the MTase further supports its relevance to enzymology.\n",
        "doc_id": "3478a5ef-78ed-4576-b931-9c8523fd0288"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the MTase protein and includes details about fluorescence polarization assays to measure the binding activity of the purified enzyme with GTP–Bodipy, indicating that in vitro enzymatic assays were performed to assess enzyme activity. The methods section describes the preparation of the reaction mixtures and the conditions under which the assays were conducted, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "578bb1ac-1f56-4422-9824-28ef4d5780e8"
      }
    ]
  },
  "24626631": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/24626631.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL23 protein in E. coli, detailing the use of chaperones to improve solubility and the methods of purification such as Ni-NTA affinity and size exclusion chromatography. Additionally, it mentions the investigation of the catalytic properties of METTL23, indicating that the authors are likely measuring enzymatic activity, which is a key aspect of experimental enzymology. The paper provides specific details about the methods used to express and purify the enzyme, which aligns with the characteristics of experimental enzymology papers.\n",
        "doc_id": "4fe1dcf7-e10e-428a-9147-b88bc5d45ba4"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL23 protein, including details about the use of E. coli for expression, the induction of protein expression with IPTG, and the purification process using Ni-NTA affinity chromatography and size exclusion chromatography. Additionally, the paper mentions the analysis of the purified protein using SDS-PAGE, which is a common method in enzymology to assess the purity and size of the protein. However, it does not explicitly mention an in vitro enzymatic assay to measure the activity of the purified enzyme, which is a key component of experimental enzymology. Nonetheless, the focus on protein expression and purification aligns with the typical methodologies found in experimental enzymology studies.\n",
        "doc_id": "79220c00-de2a-40d0-9f6c-c0278cd470f1"
      }
    ]
  },
  "21823666": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/21823666.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme Nicotinamide N-methyltransferase (NNMT), detailing the methods used for cloning, expression, and purification of the enzyme from E. coli. Additionally, the paper includes an in vitro enzymatic assay where enzyme kinetics analysis is performed to measure the activity of various mutants of NNMT, confirming the functional importance of specific active site residues. This focus on enzyme activity and the methods used to study it aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "3670ce64-d7fb-4739-8c29-c47321f227c0"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme tm-hNNMT, detailing the methods used for protein expression in E. coli, purification steps involving hydroxyapatite and Ni-NTA columns, and the conditions for crystallization. The paper also mentions the use of specific ligands (AdoHcy and NCA) during the crystallization process, which indicates an investigation into the enzyme's activity and interactions. The focus on protein purification and crystallization, along with the mention of mutagenesis to study active site residues, aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "cd0a5de1-4849-4fe2-a846-394a19b416b9"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of active site mutants of the enzyme tm-hNNMT, detailing the methods used for protein purification, including the use of a Ni-NTA Superflow Cartridge and specific lysis buffers. Furthermore, it describes in vitro enzymatic assays to measure the activity of the purified enzyme, including the composition of the assay mixture, incubation conditions, and methods for analyzing enzyme activity and kinetics. The paper also reports specific activities and kinetic parameters, which are typical components of experimental enzymology studies.\n",
        "doc_id": "015c38ef-f594-4381-a03a-548f0090e764"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the hNNMT enzyme, as well as the characterization of its activity through enzyme assays. Specifically, it mentions the use of structure-based mutagenesis to probe the functional importance of active site residues and includes detailed enzyme activity assays to compare the activities of various mutants. The paper also provides insights into enzyme kinetics, which is a key aspect of experimental enzymology.\n",
        "doc_id": "1dc02770-ab37-4efc-9333-82faf09caec6"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the investigation of enzyme activity through the use of mutagenesis on specific residues (Y20 and D197) and their effects on enzyme kinetics, specifically kcat and Km values. The paper also mentions the preparation of mutants to probe the functional roles of these side chains, which is a common approach in experimental enzymology. Additionally, the analysis of enzyme kinetics and the interaction of the enzyme with substrates (AdoMet and NCA) indicates that the paper focuses on the enzymatic activity and mechanisms, which are key components of experimental enzymology studies.\n",
        "doc_id": "36f0962d-5071-45ea-a4a6-1168cf25c952"
      }
    ]
  },
  "11850402": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/11850402.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the identification of substrates for arginine methyltransferases PRMT1 and CARM1 through the use of high-density protein filter arrays and in vitro enzymatic assays. The methods section describes the use of recombinant PRMT enzymes to perform large-scale enzyme reactions, indicating that the authors are measuring the activity of these enzymes on specific substrates. The paper also details the methylation of proteins using [³H]AdoMet, which is a clear indication of an enzymatic assay being performed to assess the activity of the purified enzymes.\n",
        "doc_id": "0a4029f4-8d0b-464c-a5cf-adc933bcdc43"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation assay using recombinant CARM1 to investigate the methylation of PABP1, which involves the overexpression and purification of the enzyme CARM1 and the subsequent measurement of its activity on specific substrates (the peptides derived from PABP1). The paper details the experimental setup, including the use of mutagenesis to identify essential residues for methylation, and it describes the results of the enzymatic assays that demonstrate the activity of CARM1 on PABP1. This aligns well with the characteristics of experimental enzymology papers, which focus on enzyme activity and assays.\n",
        "doc_id": "caf7128e-ab0a-4124-a8cd-d4c04ee2df57"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of PABP1–GST fusion proteins, which indicates that the authors are working with a specific enzyme. Additionally, the paper describes an \"in vitro methylation assay\" where methylation reactions are performed with recombinant PRMT, and it details the conditions and components of these reactions, which is characteristic of experimental enzymology. The mention of substrate and the use of [³H]AdoMet further supports that enzymatic activity is being measured, aligning with the typical structure of an experimental enzymology paper.\n",
        "doc_id": "1d2c278d-c736-4938-ac8f-679b88514441"
      }
    ]
  },
  "14508009": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/14508009.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an experimental enzymology paper. It discusses the isolation and characterization of the VTE3 locus, which encodes the enzyme MPBQ/MSBQ MT involved in tocopherol and plastoquinone synthesis. The paper mentions \"in vitro enzyme assays\" that confirmed the activity of VTE3, indicating that the authors performed enzymatic assays to measure the activity of the purified enzyme. This aligns with the typical structure of experimental enzymology papers, which include the overexpression, purification of enzymes, and subsequent activity assays.\n",
        "doc_id": "548ecb2e-8e2b-4c8a-8ba9-1c13e3072586"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the activity of the VTE3 protein, which is involved in tocopherol synthesis, and mentions the in vitro assays conducted to determine the enzyme's activity against various substrates (MPBQ and MSBQ). The paper describes the amplification of the VTE3 protein-coding region for expression in E. coli, indicating the overexpression and purification of the enzyme, which are key components of experimental enzymology. Additionally, the paper includes details about the enzymatic assays that measure the activity of the purified enzyme, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "02a3145f-3f9c-40fa-afcf-eb717597da91"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins from Synechocystis sp PCC6803 and their subsequent enzymatic activity assays using MPBQ and MSBQ as substrates. The methods section mentions the expression of proteins in E. coli, solubilization, and the use of in vitro enzyme assays to measure the activity of the purified enzymes, which are key components of experimental enzymology. Additionally, the paper provides details on the enzymatic activities and the analysis of reaction products, indicating a focus on enzyme function and characterization.\n",
        "doc_id": "0d37c15e-f372-4111-8ba8-1a583fa7c15b"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase in Escherichia coli, detailing the methods used for protein expression, solubilization, and enzyme assays. The paper includes specific information about the conditions for enzyme activity assays, such as the types and concentrations of detergents used, and it describes the enzymatic assays performed to measure the activity of the purified enzyme. This focus on enzyme expression, purification, and activity measurement is characteristic of experimental enzymology studies.\n",
        "doc_id": "1648ae8a-6c75-45e4-b494-893461ce3b0b"
      }
    ]
  },
  "11847284": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/11847284.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification and enzymatic activity of human L-isoaspartyl-O-methyltransferase (HPIMT), including details about enzyme assays that demonstrate its enzymatic activity. The paper mentions the use of highly purified recombinant HPIMT in enzyme assays, which is a key aspect of experimental enzymology. Additionally, it provides structural insights into the enzyme and its interactions with substrates, which are relevant to understanding its enzymatic function.\n",
        "doc_id": "27c8e2dc-5b59-4f5f-bb10-691d213ad284"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of the human L-isoaspartyl-O-methyltransferase (HPIMT) enzyme, detailing the methods used to amplify the coding sequence, transform E. coli, and purify the enzyme through various chromatography techniques. The paper also mentions the analysis of the purified protein using SDS-PAGE and size exclusion chromatography, which are common practices in experimental enzymology. Furthermore, it implies that the enzyme's activity could be assessed, as it references the use of model substrates, indicating that enzymatic assays may be part of the study, even if not explicitly detailed in the provided text.\n",
        "doc_id": "8f3172a1-46f5-4bd9-a9bc-c494bb7d4f50"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of a protein and the measurement of its enzymatic activity through an in vitro assay. Specifically, it details the preparation of the assay solution, the incubation conditions, and the method used to stop the reaction and analyze the activity of the purified protein. The mention of using a liquid scintillation counter to measure the results further indicates that this paper is focused on experimental enzymology, as it involves quantifying the enzymatic activity of the protein being studied.\n",
        "doc_id": "7f2d2423-62ef-47ed-936a-6cfe11e975e0"
      }
    ]
  },
  "17215513": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/17215513.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. The text mentions \"in vitro methylation experiments\" which indicates that the authors performed enzymatic assays to measure the activity of the RNA methyltransferase NSUN2. Additionally, the paper discusses the regulation of NSUN2's methyltransferase activity by phosphorylation, which is a key aspect of enzymology studies. The focus on the enzymatic function of NSUN2 and the experimental approach to assess its activity aligns well with the characteristics of an experimental enzymology paper.\n",
        "doc_id": "6874f6b2-dc2e-49b5-9f2e-49bf4f3abaf3"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification of the NSUN2 protein and includes a detailed in vitro methyltransferase assay to measure the activity of the purified enzyme. Specifically, the paper describes the use of His-NSUN2 in a methyltransferase assay where it is reacted with substrates in the presence of S-adenosylmethionine, and the results are analyzed by agarose gel electrophoresis. Additionally, the paper mentions the purification of NSUN2 from bacterial lysates and the use of various controls, which are typical components of experimental enzymology studies.\n",
        "doc_id": "e5e5e155-029e-43dc-b97d-ddaed6150f53"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the NSUN2 protein, as indicated by the mention of producing full-length wild-type and mutant forms of NSUN2 in E. coli and purifying these proteins. Furthermore, it describes an in vitro kinase assay to measure the phosphorylation activity of NSUN2 by Aurora-B, which is a key aspect of experimental enzymology. The paper details the experimental setup, including the use of specific antibodies for detection and the effects of mutations on phosphorylation, which aligns with the typical structure and focus of experimental enzymology research.\n",
        "doc_id": "722479ec-1730-4573-b363-636f4a0ee0af"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the methyltransferase activity of the NSUN2 enzyme, including details about the purification of NSUN2 and its enzymatic assays using substrates like poly(dI:dC) and tRNA to measure its activity. The paper describes how the phosphorylation status of NSUN2 affects its enzymatic activity, which is a key aspect of experimental enzymology. The methods section likely includes information on the overexpression and purification of NSUN2, as well as the in vitro assays that were performed to assess its methyltransferase activity.\n",
        "doc_id": "88af5cdb-edf3-41fa-96c2-f1e248aecfe7"
      }
    ]
  },
  "28291746": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28291746.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Zika virus RNA-dependent RNA polymerase NS5 protein, detailing the methods used for protein expression in E. coli, purification techniques including nickel-affinity chromatography and size-exclusion chromatography, and the assessment of protein purity through SDS-PAGE. Although the text does not explicitly mention an in vitro enzymatic assay, the focus on protein purification and characterization is a key aspect of experimental enzymology. The paper also describes crystallization and data collection for structural analysis, which is often a subsequent step in enzymology studies to understand enzyme function at a molecular level.\n",
        "doc_id": "4abd9dcc-ca4e-4a87-a071-a034bbbaecc7"
      }
    ]
  },
  "28533213": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28533213.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the identification of a novel methyltransferase enzyme (NANMT) responsible for N-methylnicotinate formation in Arabidopsis, and it mentions the use of enzymatic assays to reveal the N-methylation activity of this enzyme. The paper also provides insights into the evolutionary aspects of the enzyme's function and its role in the detoxification of nicotinate, which aligns with the typical focus of experimental enzymology on enzyme activity and characterization.\n",
        "doc_id": "789e1702-2165-4f96-ac3c-27c1a1825b6e"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the functional characterization of the enzyme Nicotinate N-Methyltransferase (NANMT) from Arabidopsis, including the overexpression and purification of the protein, as well as in vitro enzymatic assays to measure its activity. The paper provides specific details about the enzymatic assay, such as the use of [¹⁴C]NA and SAM as substrates, the determination of kinetic parameters (Km and Kcat values), and the comparison of activity under different conditions. These elements are characteristic of experimental enzymology studies, which focus on the analysis of enzyme activity and properties.\n",
        "doc_id": "254a742a-0be8-49ef-ae29-ed466c4df66e"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and characterization of the AtNANMT1 enzyme, including the preparation of crude protein extracts and the measurement of enzymatic activity. The paper provides specific details about the kinetic parameters (Km, Kcat, Kcat/Km) of the AtNANMT1 enzyme with substrates NA and SAM, which are essential components of an in vitro enzymatic assay. Additionally, the results indicate the enzyme's role in Tg biosynthesis and its activity in different transgenic plant lines, further supporting its classification as an experimental enzymology paper.\n",
        "doc_id": "f6205952-abe6-4c89-9494-934c50d129b3"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text mentions \"enzymatic assays with NANMT-like proteins from 10 representative plant species,\" indicating that the authors conducted in vitro assays to measure the activity of these proteins. Additionally, it discusses the catalytic efficiency of the AtNANMT1 enzyme and its activity towards specific substrates, which is a key aspect of experimental enzymology. The paper also includes details about the expression and purification of the enzyme, which are typical components of experimental enzymology studies.\n",
        "doc_id": "39859f1a-7d83-4ddf-9e4a-fbf0e0d1b991"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of plant NANMT and COMT proteins, including specific assays that measure their activity towards substrates like NA and phenylpropanoids. The paper mentions the use of [14C]NA as a substrate for the enzymatic assays, and it provides detailed results on the relative activities of various proteins, indicating that the authors performed in vitro assays to evaluate enzyme function. Additionally, the paper describes mutations in the enzyme that affect activity, which is a common approach in experimental enzymology to understand enzyme mechanisms and substrate specificity.\n",
        "doc_id": "851fce1c-a13e-4091-aad5-e0090ee67937"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of recombinant proteins, specifically AtNANMT1 and AtCOMT, and includes details about enzymatic assays such as radio-TLC analysis to measure the activity of these enzymes using specific substrates ([C]NA and SAM for NANMT activity, and [C]SAM and caffeic acid for COMT activity). The mention of negative controls and the characterization of catalytic sites further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "9a28be74-eb3b-4527-83ad-9f91ea6eaf9e"
      },
      {
        "page": 11,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the AtNANMT1 protein, as indicated by the section on generating N-terminally MBP-tagged NANMT and purifying the resulting fusion proteins using affinity chromatography. Additionally, it mentions performing NANMT assays to measure the enzymatic activity of the purified enzyme, which is a key characteristic of experimental enzymology papers. The use of techniques such as SDS-PAGE for evaluating protein purity and the detailed description of the enzymatic assays further support this classification.\n",
        "doc_id": "e752a36e-2070-42dd-ad72-9d45140a6357"
      }
    ]
  },
  "22493060": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/22493060.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Bud23-Trm112 complex, which is a protein involved in ribosome synthesis. The Methods section details the use of bacterial strains for protein expression, the construction of plasmids for expressing tagged proteins, and the purification process of the His-tagged proteins. Additionally, the paper mentions the enzymatic activity related to the methylation of rRNA, indicating that the authors likely performed in vitro assays to measure the activity of the purified enzyme complex. This focus on protein purification and enzymatic assays aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "e2513101-ec3e-4ca0-9b1d-ac3d954c42b1"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the interaction and co-purification of the proteins Trm112 and Bud23, which are involved in the methylation of 18S rRNA. The methods section includes details about the overexpression and purification of His₆-Bud23 and Trm112, as well as in vitro assays to measure the methylation activity of Bud23 in the presence of Trm112. The paper describes the use of SDS-PAGE and Western blotting to analyze the proteins, indicating that enzymatic assays were performed to assess the activity of the purified enzyme.\n",
        "doc_id": "273294ff-faad-4169-a89e-af3c6df7bb17"
      }
    ]
  },
  "1549466": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/1549466.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. The authors discuss the expression and purification of two proteins, MTF1 and ABF2, which are involved in mitochondrial transcription initiation. They specifically mention that MTF1 was expressed in Escherichia coli to obtain significant amounts of the protein and that ABF2 was purified from a yeast mitochondrial extract. Furthermore, the paper describes the use of in vitro transcription assays to test the effects of these proteins on transcription initiation, which is a key aspect of experimental enzymology.\n",
        "doc_id": "6e96d0ed-f9ec-43b7-93ef-7440ba4ad257"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the yeast mtRNA polymerase (RPO41) and includes details about in vitro transcription assays to measure the activity of the enzyme. The Methods section describes the construction of plasmids for overexpression, the use of specific microbial strains, and the conditions for the transcription assays, which are key components of experimental enzymology. The mention of quantifying synthesized RNA and the specific conditions for the enzymatic reactions further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "56e70cc6-e587-4791-bc1e-978b22def19b"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the ABF2 protein and the mtRNA polymerase from yeast, detailing the methods used for purification, including various chromatography techniques (Heparin Sepharose, Blue Sepharose, and DEAE-Sephacel). Additionally, it mentions the enzymatic assays performed to measure the activity of the purified enzymes, specifically the nonspecific transcription activity of RNA polymerase and the specific mtRNA polymerase activity on the yeast mitochondrial 14S rRNA promoter. These elements indicate that the paper focuses on experimental enzymology, as it includes both the purification of enzymes and the assessment of their activity through in vitro assays.\n",
        "doc_id": "cd30df29-b059-40cb-ac5d-b232a568346f"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the MTF1 protein in E. coli, detailing the use of IPTG to induce expression and the subsequent purification steps, including gel filtration and chromatography techniques. Additionally, it describes in vitro transcription assays to measure the activity of the purified enzyme (RPO41 and rMTF1), which is a key characteristic of experimental enzymology papers. The methods section includes specific details about the enzymatic assays performed, indicating that the paper focuses on the functional analysis of the enzymes involved.\n",
        "doc_id": "47e5bfa1-6802-4f38-be8d-fb3b6ee8871c"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the protein MTF1, which is identified as a specificity factor for mitochondrial RNA polymerase. The paper details the methods used to express MTF1 in E. coli, purify it, and then perform an in vitro transcription assay to measure its activity. Specifically, it mentions the use of SDS-polyacrylamide gel electrophoresis for protein analysis, the elution of proteins from the gel, and the assessment of transcription initiation activity, which are all key components of experimental enzymology. The results demonstrate the functional role of MTF1 in transcription, further emphasizing the enzymatic aspect of the study.\n",
        "doc_id": "8c74ed24-0447-44d5-bde5-a03409953fe7"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the ABF2 protein and its role in mitochondrial transcription, including the use of in vitro assays to measure its DNA binding and transcription activity. The paper mentions the purification of mtRNA polymerase and the specific enzymatic activity on the 14S rRNA promoter, which indicates that the authors conducted enzymatic assays to assess the activity of the proteins involved. This aligns with the characteristics of experimental enzymology papers, which typically include the overexpression, purification, and activity measurement of enzymes.\n",
        "doc_id": "a87c25a4-fc2b-468c-9868-88fe68962da9"
      }
    ]
  },
  "15247431": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/15247431.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the cloning, expression, and purification of the YfcK protein, which is identified as the bifunctional enzyme MnmC. The paper specifically mentions that the authors demonstrated the enzyme's activity in catalyzing the formation of the hypermodified nucleoside mnm⁵s²U in tRNA, indicating that an in vitro enzymatic assay was performed to measure the activity of the purified enzyme. This aligns with the characteristics of experimental enzymology papers, which typically include the overexpression and purification of enzymes followed by enzymatic assays to assess their activity.\n",
        "doc_id": "47dc3dbd-e3af-4fed-8df6-bf570b85b3d3"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the YfcK protein, which is suggested to be the MnmC enzyme involved in tRNA modification. The Methods section describes the cloning of the yfcK gene into a pET28a expression vector, the induction of protein expression in E. coli, and the purification of the His-tagged protein using immobilized metal ion chromatography and ion-exchange chromatography. Furthermore, the paper details an in vitro enzymatic assay where the purified YfcK protein is incubated with tRNA and radiolabeled AdoMet to assess its tRNA modification activity, which is a key characteristic of experimental enzymology studies.\n",
        "doc_id": "ce5299bb-7e8a-4a98-9333-d19912437980"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of the recombinant YfcK protein and describes an in vitro enzymatic assay where the enzyme catalyzes the formation of mnm⁵s²U in tRNA. The methods section mentions the purification process using SDS-polyacrylamide gel and the subsequent enzymatic activity measured through autoradiography and thin-layer chromatography (TLC). These details indicate that the paper focuses on experimental enzymology, specifically the characterization of an enzyme's activity after purification.\n",
        "doc_id": "1fb6b738-38d8-4862-931b-a7be917bbd6c"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the cloning, expression, and purification of the E. coli YfcK protein, which indicates that the authors are working with a specific enzyme. The mention of using PCR to amplify the gene, the incorporation of restriction sites for cloning, and the use of an expression vector (pET28a) all point to the overexpression and purification of the enzyme. Additionally, the paper proposes a tentative mechanism for the enzymatic formation of mnm⁵s²U from cmnm⁵s²U, which suggests that there is an in vitro enzymatic assay involved to measure the activity of the purified enzyme. Overall, these details align well with the characteristics of an experimental enzymology paper.\n",
        "doc_id": "d8fba64b-af9e-4191-943e-a6e53de7ed06"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of a recombinant His-tagged protein (H6YfcK) in E. coli, detailing the methods used for protein expression, lysis, and purification through various chromatography techniques. Additionally, it describes an in vitro enzymatic assay where the purified H6YfcK protein is incubated with total tRNA and [methyl-¹⁴C]AdoMet to analyze the resulting nucleotides, indicating the measurement of enzymatic activity. This combination of protein purification and enzymatic assay is characteristic of experimental enzymology papers.\n",
        "doc_id": "ddd27d77-dff0-410c-8d83-302706c459fd"
      }
    ]
  },
  "31493651": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31493651.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The Methods section describes the overexpression and purification of the CHIKV HVD protein, detailing the use of E. coli for protein production, the introduction of tags for purification, and the specific purification steps including HisTrap HP column and size exclusion chromatography. Additionally, the paper discusses the use of NMR spectroscopy to study protein interactions, which is relevant to understanding enzymatic activity and interactions, although it does not explicitly mention an in vitro enzymatic assay. The focus on protein purification and characterization aligns with the typical structure of experimental enzymology papers.\n",
        "doc_id": "90d0b92c-bbf4-4b7b-addb-b7528f0ac103"
      }
    ]
  },
  "24838010": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/24838010.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme CcsB, which is a Baeyer-Villiger monooxygenase, and describes an in vitro enzymatic assay to measure its activity. The authors detail the cloning, expression, and purification of CcsB from Escherichia coli, and they perform an in vitro reaction with CcsB and a substrate (compound 7) in the presence of NADPH and FAD, demonstrating the enzyme's catalytic activity. This aligns with the characteristics of experimental enzymology papers, which typically include methods for enzyme purification and assays to measure enzymatic activity.\n",
        "doc_id": "06e56699-31aa-4a30-bbc6-5862b196f56f"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzyme CcsB and its role in converting a ketone into a carbonate, which is a clear indication of enzymatic activity. The paper describes the experimental setup, including the use of a ΔccsB-37 strain to confirm the catalytic role of CcsB in the reaction, and mentions the purification and characterization of compounds involved in the enzymatic process. Additionally, it details the reaction conditions and the effects of various substrates on the enzyme's activity, which are typical elements found in experimental enzymology studies.\n",
        "doc_id": "056f9cd6-d126-4cb3-a245-89963802a982"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro reaction conditions for the enzyme CcsB, including the use of specific substrates and cofactors (e.g., NADPH, FAD) in the enzymatic assays. The paper also presents HPLC analysis of the products formed during the enzymatic reactions, indicating that the authors measured the activity of the purified enzyme. Additionally, it mentions the use of a CcsB mutant and control reactions, which are typical components of experimental enzymology studies aimed at understanding enzyme function and kinetics.\n",
        "doc_id": "377b88d2-8df7-454d-acc2-90fd2224e53d"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme CcsB, detailing the methods used for protein expression in E. coli, including the use of IPTG for induction and the purification process using Anti-Flag M1 Agarose Affinity Gel. Furthermore, it includes an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically monitoring the conversion of substrates into products using LC/MS. This combination of protein purification and enzymatic activity measurement is characteristic of experimental enzymology studies.\n",
        "doc_id": "3f1ad9a8-6a31-4625-83e3-1f986e39fe99"
      }
    ]
  },
  "18367445": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/18367445.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the human spermine synthase (SpmSyn) enzyme, detailing the methods used for its expression in E. coli, purification through affinity chromatography, and subsequent crystallization. The paper also mentions the use of site-directed mutagenesis to identify key residues in the active site, which is a common approach in enzymology to study enzyme function and mechanism. The focus on the enzyme's structure and its implications for catalysis further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "0bab12f1-f408-4c71-b0c6-7bda99f6dc8c"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme human spermine synthase (SpmSyn), detailing the purification process using ion-exchange chromatography and the crystallization of the purified protein. Additionally, it includes in vitro enzymatic assays to measure the activity of the enzyme, specifically the production of [³⁵S]MTA from [³⁵S]dcAdoMet, and describes the conditions under which these assays were performed, including the use of specific buffers and substrates. The paper also mentions the determination of kinetic constants, which is a common aspect of experimental enzymology studies.\n",
        "doc_id": "5d9ee33e-bc72-4bd4-b610-456196ffd0e5"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the generation of deletion mutants of human spermine synthase (SpmSyn) and tests their structural properties and enzymatic activity. The paper specifically mentions that deletions of certain domains led to a complete loss of activity, indicating that the authors performed in vitro enzymatic assays to measure the activity of the purified enzyme. This aligns with the typical characteristics of experimental enzymology papers, which include the overexpression, purification of enzymes, and subsequent activity assays.\n",
        "doc_id": "ae39a694-df6b-4f8e-9786-4be988f20d89"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of human spermine synthase (SpmSyn) and includes details about the activity of truncated protein fragments, which suggests that in vitro enzymatic assays were performed to measure the activity of the purified enzyme. The paper mentions the activity percentages of different constructs and their interactions, indicating that the authors conducted experiments to assess the enzymatic function of these proteins. Additionally, the paper describes the active site of SpmSyn and its interactions with substrates, which is a common focus in experimental enzymology studies.\n",
        "doc_id": "1d564069-dda2-4bc9-9225-c58ae4db96b1"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the kinetic properties of human spermine synthase (SpmSyn) mutants, including measurements of kcat and Km values, which are essential for understanding enzyme activity. The paper also mentions site-directed mutagenesis to analyze the catalytic mechanism, indicating that the authors performed experiments to assess the effects of specific mutations on enzyme function. Additionally, the paper includes details about the crystal structure of the enzyme and its interaction with substrates, which is relevant to enzymatic assays and understanding enzyme mechanisms. Overall, the focus on kinetic properties and mutational analysis aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "a954aa5b-c83b-4eda-a2a0-75f6a2d3cdb2"
      }
    ]
  },
  "22984289": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/22984289.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the import and sorting of mitochondrial proteins, specifically focusing on the enzymatic activity of proteins in the intermembrane space (IMS). The paper mentions biochemical assays to confirm the localization of IMS proteins and describes in vitro experiments involving the import of preproteins into isolated mitochondria, which is a key aspect of experimental enzymology. Additionally, it details the use of radiolabeled precursor proteins and various biochemical techniques, such as SDS-PAGE and BN-PAGE, to analyze protein interactions and activities, indicating a focus on enzymatic assays and protein characterization.\n",
        "doc_id": "0adc0708-b9b0-4e44-b8d2-4fcd2809b08d"
      }
    ]
  },
  "32558197": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/32558197.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the reconstitution of the 20-O-methylation activity of the FTSJ1-WDR6 complex in vitro, which indicates that the authors performed an enzymatic assay to measure the activity of the enzyme. The paper also mentions the catalytic activity and the specific RNA substrates involved, which are key components of experimental enzymology. Additionally, the focus on the enzymatic activity and its implications for tRNA modifications aligns with the typical content found in experimental enzymology studies.\n",
        "doc_id": "3091c6fd-945c-4550-a8d2-0fe219310681"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. The authors discuss the purification of the FTSJ1 protein using a baculovirus/insect cell system and demonstrate its catalytic activity in vitro, specifically its ability to produce Nm34 from specific tRNA substrates. The paper also details the interaction between FTSJ1 and WDR6, and how FTSJ1 binds to S-adenosyl-L-methionine (SAM) as a methyl donor, which is a key aspect of enzymatic activity. The focus on the enzymatic assay and the characterization of the enzyme's function aligns well with the criteria for experimental enzymology papers.\n",
        "doc_id": "a982be80-81c6-4852-8ff2-4d9b65b389f9"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the purification of GST-WDR6 from baculovirus-infected insect cells and tests the catalytic activity of the mixture of FTSJ1 and WDR6 in vitro. The mention of measuring the methylation activity on tRNAPhe(GAA) as a substrate indicates that the authors are conducting enzymatic assays to evaluate the activity of the purified enzyme, which is a key characteristic of experimental enzymology papers.\n",
        "doc_id": "30373227-ee83-40af-bac0-d495236bd512"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the in vitro enzymatic activity of the FTSJ1-WDR6 complex, specifically its role in catalyzing the Gm34 modification of tRNA. It describes experiments where tRNA substrates are incubated with the FTSJ1-WDR6 complex to measure the formation of Gm, indicating that the authors performed enzymatic assays to assess the activity of the enzyme. Additionally, the paper mentions the construction of tRNA mutants and the analysis of their modifications, which further supports the experimental enzymology focus. The presence of detailed methods for measuring enzymatic activity and the characterization of the enzyme's function aligns well with the criteria for an experimental enzymology paper.\n",
        "doc_id": "93ceeee5-c917-405f-9da8-e19f9bf80fd0"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro enzymatic activity of the FTSJ1-WDR6 complex on tRNA substrates, specifically focusing on the catalysis of Gm34 formation on tRNAPhe(GAA) with m1G37. The paper includes details about the purification of tRNA substrates and the use of UPLC-MS/MS analysis to quantify the enzymatic products, which indicates that enzymatic assays were performed to measure the activity of the enzyme. The mention of incubating tRNA with FTSJ1-WDR6 and analyzing the resulting modifications further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "5766b92a-18f2-4455-90ed-3d858509b0e9"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro enzymatic assays of FTSJ1-WDR6, specifically measuring the activity of the enzyme on various tRNA substrates. The paper details the experimental setup, including the use of T7 RNA polymerase for transcription and the modification of tRNAs, which are key components of experimental enzymology. Additionally, it mentions the results of these assays, indicating the substrates of FTSJ1-WDR6 and their respective modifications, which aligns with the typical focus of experimental enzymology papers on enzyme activity and substrate interactions.\n",
        "doc_id": "867e0b86-2b8c-4e85-a60a-27c90bef4fac"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the reconstitution of the 20-O-methylation activity of the enzyme FTSJ1 in vitro, which indicates that the authors performed an enzymatic assay to measure the activity of the purified enzyme. The paper mentions the catalytic role of FTSJ1 and its interaction with WDR6, which suggests that the authors investigated the enzymatic mechanism and substrate recognition. Additionally, the paper includes details about the modifications of tRNA mediated by FTSJ1, which is a common focus in experimental enzymology studies.\n",
        "doc_id": "4655acd8-acc6-4234-b815-b7337ef2766d"
      },
      {
        "page": 15,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the FTSJ1 protein, which is indicated by the section detailing the expression of the FTSJ1-His fusion protein in High Five insect cells and the subsequent purification steps using Ni2+-NTA chromatography. Additionally, the paper implies that there are follow-up experiments planned, which likely include in vitro enzymatic assays to measure the activity of the purified enzyme, although the specific assays are not detailed in the provided text. The methods described align with typical practices in experimental enzymology, focusing on protein handling and preparation for enzymatic activity analysis.\n",
        "doc_id": "cb6a5da5-de0a-44f2-846b-7fd6f683df86"
      },
      {
        "page": 16,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins/enzyme (GST-WDR6 and His6-tagged TrmD) using baculovirus-mediated transduction and E. coli expression systems, respectively. The methods section details the purification processes, including the use of glutathione HiCap matrix columns and Ni-NTA Superflow resin. Additionally, the paper describes in vitro enzymatic assays, such as the tRNA methyl transfer assay, where the activity of the enzymes is measured by their ability to methylate tRNA, indicating a clear focus on enzymatic activity and characterization.\n",
        "doc_id": "fd058e63-ac25-45c3-947e-5e4f24a02d27"
      }
    ]
  },
  "16946471": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/16946471.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme PhzM, detailing the methods used for protein expression in E. coli, the purification process involving various chromatography techniques, and the characterization of the enzyme. The paper also mentions the enzymatic activity related to the biosynthesis of pyocyanin, indicating a focus on the enzyme's function. The detailed methodology for producing and purifying the enzyme, along with the context of its biological role, aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "b7f9938a-0886-427a-9749-61f323b000c0"
      }
    ]
  },
  "35294288": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/35294288.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of proteins, specifically mentioning the use of a pET28a vector for cloning and the expression of recombinant proteins in Escherichia coli. The methods include purification through Ni-chelating affinity chromatography, which is a common technique in enzymology for isolating proteins. Additionally, the paper describes the preparation of proteins for assays, indicating that enzymatic activity measurements may be part of the study, even though the specific enzymatic assays are not detailed in the provided text.\n",
        "doc_id": "3c1bbb6c-9c13-4c69-860f-e4778fadd7b7"
      }
    ]
  },
  "20376845": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/20376845.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the plant halomethyltransferase enzyme (AtHTMT), detailing the cloning of the gene, the use of a C-terminal His tag for purification, and the subsequent enzymatic assays that measure the activity of the purified enzyme with various nucleophiles. The paper also describes the structural analysis of the enzyme and its active site, which is a common focus in experimental enzymology studies. The mention of specific mutations and their effects on enzyme activity further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "253d1ca3-f7db-49f1-b297-99fbad242226"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses enzyme kinetic data for various AtHTMT (Arabidopsis thaliana halomethyl transferase) variants, including measurements of kinetic parameters such as K_m and V_max for different nucleophiles. The mention of enzyme activity and kinetic data indicates that the paper involves the study of enzyme function and performance, which is a key aspect of experimental enzymology. Additionally, the context suggests that the paper likely includes methods related to the purification and characterization of the enzyme, which are typical components of experimental enzymology studies.",
        "doc_id": "8123643f-384b-45b1-add5-f9eff308bea4"
      }
    ]
  },
  "32198201": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/32198201.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification and enzymatic activity of the EndoU enzyme, including a specific RNA cleavage assay that measures the enzyme's activity. The Methods section details the conditions under which the enzyme was tested, such as the reaction buffer composition and the temperature, as well as the techniques used to analyze the reaction products, indicating a focus on in vitro enzymatic assays. This aligns with the characteristics of experimental enzymology papers, which typically involve the overexpression, purification, and activity measurement of enzymes.\n",
        "doc_id": "32b90302-4e27-4702-94b2-d66b7e010209"
      }
    ]
  },
  "27383630": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/27383630.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the heterologous expression and purification of the G3BP-1 protein, which is a key step in experimental enzymology. The methods section details the use of immobilized metal affinity chromatography (IMAC) and size exclusion chromatography (SEC) for purification, as well as the cleavage of a poly-histidine tag using TEV protease. Additionally, the paper mentions the preparation of a protein complex (G3BP-1:nsP3-25) for crystallization, which indicates a focus on the structural and functional analysis of the enzyme. Although the paper does not explicitly mention an in vitro enzymatic assay, the detailed purification and characterization of the protein suggest that it is part of an experimental enzymology study aimed at understanding the enzymatic functions of the proteins involved.\n",
        "doc_id": "18c411fe-b89f-4314-ba34-7c65e1750c5a"
      }
    ]
  },
  "33693809": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/33693809.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the METTL18 protein, which is identified as a histidine-specific methyltransferase. The paper mentions that recombinant METTL18 was able to methylate a specific protein (RPL3) in nuclear extracts and isolated ribosomes, indicating that an in vitro enzymatic assay was performed to measure the activity of the purified enzyme. Additionally, the study explores the functional relevance of METTL18 in ribosome biogenesis and function, which is a key aspect of experimental enzymology.\n",
        "doc_id": "f747bdca-9fe7-448f-95a8-b47864d0b770"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the METTL18 protein, which is identified as a methyltransferase (MTase) responsible for introducing methylation at a specific position in the ribosomal protein RPL3. The paper details the methods used for gene cloning, mutagenesis, and transient transfection of HeLa cells, which are typical procedures in experimental enzymology. Additionally, it mentions the biochemical assays that demonstrate the methylation activity of METTL18 on RPL3, indicating that the authors conducted in vitro enzymatic assays to measure the activity of the purified enzyme.\n",
        "doc_id": "d5e68237-4a72-4775-be4f-0ebf2d60ed99"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the expression and purification of the METTL18 protein, which is a key aspect of experimental enzymology. The paper details the cloning of the METTL18 ORF into a plasmid, transformation into E. coli, and induction of protein expression, followed by the isolation of the His-tagged METTL18 protein. Additionally, it mentions the use of various buffers and conditions for protein purification, which are typical in enzymology studies. The focus on the enzymatic activity of METTL18, as indicated by the mention of its role in methyltransferase activity, further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "8ab09829-33e2-48dd-8011-b09d8a4c7ac7"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the METTL18 protein, which is a methyltransferase, and includes a detailed in vitro methyltransferase assay to measure the activity of the purified enzyme. The methods section describes the purification process using Ni-NTA-agarose and the subsequent enzymatic assay involving [3H]AdoMet, indicating that the authors are measuring the enzymatic activity of METTL18. This aligns with the characteristics of experimental enzymology papers, which focus on enzyme purification and activity assays.\n",
        "doc_id": "6ad355b3-61bf-4d8c-a98a-eb639b89cdde"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL18 protein, specifically mentioning the expression of a truncated variant of METTL18 in E. coli and its subsequent purification. Furthermore, the paper describes an in vitro enzymatic assay to measure the methyltransferase activity of the purified METTL18 using a cell extract from METTL18 knockout cells, which is a key characteristic of experimental enzymology studies. The results include the detection of methylated proteins, indicating that the enzymatic activity of METTL18 was assessed in the experiments.\n",
        "doc_id": "e6594e6d-6a44-4406-b6d7-e1846081312f"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the METTL18 enzyme, as well as its enzymatic activity in vitro, specifically the methylation of a nuclear-associated protein. The methods section describes the use of [3H]AdoMet and the analysis of methylation through SDS-PAGE and fluorography, which are typical techniques used to measure enzyme activity. Additionally, the paper provides evidence that the enzymatic activity is dependent on METTL18, as shown by the results with the D217A mutation, which abrogates its activity. This focus on enzyme purification and activity measurement aligns well with the characteristics of experimental enzymology.\n",
        "doc_id": "8d882e26-7031-4331-bf1c-562f4df72d15"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation of ribosomal protein RPL3 by the enzyme METTL18, detailing the experimental setup where recombinant METTL18 is used to methylate RPL3 in the presence of [3H]AdoMet. The paper describes the purification of ribosomal proteins and the use of SDS-PAGE and fluorography to visualize the methylation, which are typical methods in experimental enzymology. Additionally, it mentions the comparison of the activity of the wild-type METTL18 and its inactive mutant, providing clear evidence of enzymatic activity being measured.\n",
        "doc_id": "45794359-dc13-4dc8-bcdb-f6015192838c"
      },
      {
        "page": 12,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the enzymatic activity of METTL18, specifically its role as a histidine-specific methyltransferase (MTase) that introduces a 3MH modification at His-245 in human RPL3. The paper mentions the purification of recombinant METTL18 and its ability to methylate RPL3 in cellular extracts, which indicates an in vitro enzymatic assay. Additionally, it describes the effects of METTL18 knockout on ribosome formation and translation dynamics, further emphasizing the functional analysis of the enzyme's activity. The presence of detailed experimental methods related to enzyme activity and the analysis of its substrates supports the classification of this paper as an experimental enzymology study.\n",
        "doc_id": "78662e94-ec8a-4711-abf9-7991784de94c"
      }
    ]
  },
  "24036117": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/24036117.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of mitochondrial methyltransferases (RNMTL1, MRM1, and MRM2) in Escherichia coli, as indicated by the mention of using a C-terminal His tag and induction with isopropyl 1-thio-β-D-galactopyranoside. The paper also describes the purification process using HisTrap columns, which is a common method in enzymology to isolate proteins. Furthermore, it implies that the authors are investigating the enzymatic activity of these proteins in relation to rRNA methylation, which aligns with the focus of experimental enzymology on measuring enzyme activity.\n",
        "doc_id": "0cee245f-6de4-43e0-ba28-f16e2a6c9753"
      }
    ]
  },
  "31147608": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31147608.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. It discusses the characterization of Rv0187, an O-methyltransferase, including the determination of high-resolution crystal structures in the presence and absence of cofactors. The paper also mentions the examination of in vitro activities, which indicates that enzymatic assays were performed to measure the activity of the purified enzyme against various catechol-like compounds. This focus on enzyme activity and the biochemical characterization aligns well with the criteria for experimental enzymology papers.\n",
        "doc_id": "e944a88f-2927-4051-a4f6-cadfc6ff0b24"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the enzyme Rv0187 from Mycobacterium tuberculosis, as indicated by the mention of testing several expression constructs and the use of size-exclusion chromatography for purification. Additionally, the paper describes an in vitro methyl transfer activity assay to examine the substrate specificity and regioselectivity of the enzyme, which is a key component of experimental enzymology. The combination of structural analysis and biochemical assays provides valuable insights into the enzyme's function, aligning well with the characteristics of experimental enzymology research.\n",
        "doc_id": "058ff30a-b0c4-4534-963f-89a244176cb5"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the enzyme Rv0187, as indicated by the mention of \"recombinant Rv0187\" expressed in E. coli and the analysis of copurified metabolites. Additionally, it includes an in vitro enzymatic assay to measure the binding of SAM to the enzyme using isothermal titration calorimetry (ITC), which is a common method to assess enzyme-substrate interactions. The paper also provides thermodynamic parameters related to the binding process, further supporting its focus on enzymatic activity.\n",
        "doc_id": "7f60a50f-8edc-48fa-bc22-de5eb8433156"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro activity of the enzyme Rv0187, including the measurement of its methyltransfer activity on various substrates, which is a key aspect of experimental enzymology. The paper details the use of HPLC and LC-MS analyses to verify the enzymatic activity, and it describes the effects of temperature and a specific mutation (K142A) on the enzyme's activity and regioselectivity. Additionally, it mentions the analysis of steady-state kinetics and the metal dependency of the enzyme, which are common topics in experimental enzymology studies.\n",
        "doc_id": "9532362a-7eaf-4338-9414-3d40e9e09f3e"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the screening of catechol-like compounds as substrates for the methyltransfer activity of the enzyme Rv0187, which indicates that the authors have purified the enzyme and are measuring its activity in vitro. The mention of using recombinant Rv0187 for methyltransfer reactions and the use of HPLC or LC-MS for analysis further supports that this paper involves experimental enzymology, as it includes both the characterization of the enzyme and the assessment of its enzymatic activity.\n",
        "doc_id": "2d6db3ac-f42a-43d1-9357-6c0f283a0e69"
      },
      {
        "page": 8,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro activity and regioselectivity of the enzyme Rv0187, including specific details about the enzymatic reactions, such as apparent conversion rates of substrates and kinetic parameters (K and k values). The paper also mentions the use of a K142A mutant enzyme and provides quantitative data on the efficiency of the enzymatic reactions, which are key components of experimental enzymology. Additionally, the mention of crystal structures and sequence similarity networks supports the characterization of the enzyme, further indicating that the focus is on enzymatic activity and properties.\n",
        "doc_id": "967f1bab-6a25-4c90-8f49-aa3bb897d3c0"
      },
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the cloning and purification of the Rv0187 enzyme from Mycobacterium tuberculosis, which is a key aspect of experimental enzymology. The Methods section details the use of polymerase chain reaction (PCR) for gene amplification and the insertion of the gene into expression vectors, indicating the overexpression of the enzyme. Additionally, the paper mentions the enzyme's activity in methylating various substrates in vitro, which aligns with the typical focus of experimental enzymology on measuring enzyme activity through in vitro assays. The discussion of kinetic parameters and substrate specificity further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "46c6b8bb-6d59-47e5-9b2d-3044a7e2ed4a"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Rv0187 enzyme, detailing the methods used for transformation of E. coli, induction of protein expression, and purification steps using Ni-NTA chromatography and gel filtration. Additionally, it describes an in vitro enzymatic assay to measure the methylation activity of the purified enzyme, including the reaction conditions, substrate concentrations, and the use of HPLC for analyzing the reaction products. The paper also mentions the calculation of kinetic parameters, which is a common aspect of experimental enzymology studies.\n",
        "doc_id": "0a3ae6ab-c70f-4729-ada4-094b31ddd974"
      }
    ]
  },
  "31043742": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/31043742.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 9,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the human NNMT enzyme, detailing the cloning, transformation into E. coli, and purification processes using techniques such as immobilized metal affinity chromatography and size exclusion chromatography. Additionally, it includes an in vitro enzymatic assay to measure the activity of the purified NNMT enzyme using the Promega MTase-Glo Methyltransferase Assay kit, which is a clear indication of experimental enzymology. The paper provides specific details about the assay conditions, including the components of the reaction and the method of measuring enzymatic activity, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "3d475c46-2dcf-4946-b56c-862b7eb55e44"
      },
      {
        "page": 24,
        "text": "\nYes: this paper is a good example of an enzymology paper. It includes an \"in vitro NNMT enzymatic activity assay\" which indicates that the authors are measuring the activity of the NNMT enzyme in response to treatment with an inhibitor (NNMTi). This suggests that the paper discusses the purification and functional analysis of the enzyme, which is a key aspect of experimental enzymology. Additionally, the mention of experimental replicates and specific assays points to a systematic approach typical of experimental studies in enzymology.\n",
        "doc_id": "aa34933e-b8e6-44d9-84c7-0f161ed25e9b"
      }
    ]
  },
  "26529540": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/26529540.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. The Methods section describes the cloning, expression, and purification of the human PRMT8 enzyme, including details about the use of baculovirus and E. coli for protein expression, as well as the purification process involving Ni-NTA resin and size exclusion chromatography. Additionally, the paper discusses the characterization of PRMT8 oligomers and the structural determination of the enzyme, which are common practices in experimental enzymology. The focus on the enzyme's activity and interactions, particularly in relation to methylation events, further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "891c3bbe-9fe2-4def-83c8-8b9d1a930ea0"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation activity assay involving the recombinant H2A/His-tagged H2B dimer and NIFK with PRMTs, which indicates the measurement of enzymatic activity. The paper details the incubation of these proteins in the presence of [3H]AdoMet and describes the detection of methylation through fluorography, which is a common method used to assess enzyme activity. Additionally, the paper mentions the overexpression and purification of proteins, which are key components of experimental enzymology studies.\n",
        "doc_id": "c32ededf-b5ea-49a2-9a96-431c9d427c68"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the purification and characterization of the enzyme tPRMT8, including its oligomerization state and enzymatic activity. The methods section mentions the use of SDS-PAGE and native-PAGE to analyze the purified protein, which indicates that the authors are measuring the activity and structural properties of the enzyme. Additionally, the paper references the importance of dimerization and tetramerization for enzymatic activity, which is a key aspect of experimental enzymology. The presence of techniques like size exclusion chromatography and analytical ultracentrifugation further supports the classification as an experimental enzymology paper, as these methods are commonly used to study enzyme properties and activities.\n",
        "doc_id": "e02afbc1-76ff-48fc-9c04-928d236682df"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the in vitro methylation studies that demonstrate the activity of the enzyme PRMT8 on the substrate NIFK, indicating that NIFK is a methylation target of PRMT8 and tPRMT8. The paper also mentions the use of mass spectrometry to analyze the methylation of specific arginine residues, which is a common method in enzymology to confirm enzyme activity. Additionally, the paper describes the engineering of a chimera to study the effects on methylation, further emphasizing the experimental approach to understanding enzyme function.\n",
        "doc_id": "f3e8d040-5145-4d97-81dd-f229b3f9c058"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the methylation activity of the enzyme PRMT8 and its interaction with various protein substrates, including NIFK and the H2A/H2B dimer. The paper includes details about in vitro methylation assays, as evidenced by the mention of \"methylation assay of tPRMT8 and tPRMT8C against NIFK\" and the use of SDS-PAGE and Coomassie staining to demonstrate the methylation activity. This indicates that the authors are measuring the enzymatic activity of the purified enzyme, which is a key characteristic of experimental enzymology papers.\n",
        "doc_id": "85c2cb9d-5e98-40d3-bfcf-088b5424c919"
      }
    ]
  },
  "28369540": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/28369540.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an experimental enzymology paper. The study discusses the overexpression and purification of the OsTrm13 protein, which is identified as a rice tRNA nucleoside methyltransferase. It specifically mentions that the purified OsTrm13 protein catalyzed the formation of 2′-O-methyladenosine (Am) on tRNA-Gly-GCC in vitro, indicating that an enzymatic assay was performed to measure the activity of the purified enzyme. This aligns with the characteristics of experimental enzymology papers, which typically include the purification of an enzyme and an in vitro assay to assess its activity.\n",
        "doc_id": "06d51b8b-e77d-47e7-bb52-804777ca33bb"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the OsTRM13 protein, which is indicated by the detailed methods for cloning the cDNA into a vector, transforming it into BL21 cells, and purifying the resulting fusion protein using GST resin. Additionally, the paper describes an in vitro enzymatic assay for tRNA methylation, where the purified OsTRM13 protein is used as a methyltransferase in the presence of tRNA and AdoMet. Furthermore, it mentions the measurement of enzymatic activities of superoxide dismutase and peroxidase in transgenic rice, which aligns with the typical focus of experimental enzymology on enzyme activity assays.\n",
        "doc_id": "76e7ad19-5299-49b6-ab38-62045b9da669"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the OsTrm13 protein, which is indicated by the mention of expressing it as an N-terminal fusion protein with GST and purifying it after ProScission Protease cleavage. Additionally, the paper describes an in vitro enzymatic assay where the purified OsTrm13 protein is used to methylate tRNA substrates in the presence of AdoMet as a methyl donor, and the products are analyzed by LC-MS. This clearly demonstrates the measurement of enzymatic activity, which is a key characteristic of experimental enzymology papers.\n",
        "doc_id": "c79becc5-3dda-4357-ad5f-c68b183425ad"
      },
      {
        "page": 7,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the OsTRM13 protein, as indicated by the mention of \"in vitro expression of GST-tagged OsTrm13 and purification of tag-free OsTrm13 protein.\" Additionally, it describes an in vitro enzymatic assay where the enzyme's activity is measured by assessing its ability to methylate tRNA, as shown in the results with \"in vitro methylation with tRNA-Gly-C4\" and the analysis of nucleoside modifications. These details confirm that the paper involves experimental enzymology techniques.\n",
        "doc_id": "3dc62e92-c864-4b07-9953-3c559353246f"
      },
      {
        "page": 10,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the characterization of the OsTrm13 protein, which is identified as an AdoMet-dependent methyltransferase (MTase) that catalyzes modifications of tRNA. The paper mentions the enzymatic activity of OsTrm13 in modifying specific tRNA substrates, indicating that in vitro enzymatic assays were likely performed to measure this activity. Additionally, the paper provides details about the expression levels of the enzyme and its role in salt stress tolerance, which aligns with the typical focus of experimental enzymology on enzyme activity and function.\n",
        "doc_id": "24df7615-14ff-424f-bd61-262f31b1383b"
      }
    ]
  },
  "23966862": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/23966862.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. The paper discusses the enzymatic activity of the coronavirus nsp14-ExoN, which is described as having exoribonuclease activity that is essential for high-fidelity replication of the virus. It details the methods used to assess the enzyme's activity, including the use of ribavirin (RBV) and 5-fluorouracil (5-FU) to evaluate the sensitivity of viruses lacking ExoN activity. The paper also mentions the purification and characterization of the enzyme, as well as in vitro assays to measure the effects of these compounds on viral replication and enzyme activity. This aligns with the characteristics of experimental enzymology, which typically involves the overexpression, purification, and activity measurement of enzymes.\n",
        "doc_id": "168e5016-4b09-4894-a25b-0a0d89f5fcd3"
      }
    ]
  },
  "22156523": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/22156523.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an enzymology paper. The Methods section describes the cloning, expression, and purification of the JEV E protein, which indicates that the authors have overexpressed and purified a protein. Although the paper primarily focuses on the crystal structure of the protein, the mention of expression and purification suggests that the authors may have conducted enzymatic assays to study the activity of the purified enzyme, which is a key aspect of experimental enzymology.\n",
        "doc_id": "5ba7dd4d-9848-4099-a7b4-9110bc11c3cf"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the JEV E protein, detailing the methods used for cell lysis, protein refolding, and purification through various chromatography techniques. The paper describes the use of recombinant DNA technology to express the protein in E. coli, the solubilization of inclusion bodies, and the subsequent purification steps, which are all key components of experimental enzymology. Additionally, while the paper primarily focuses on structural analysis and crystallization, the detailed methodology for protein purification and the mention of protein activity assays suggest that it is rooted in enzymology practices.\n",
        "doc_id": "c4772550-b231-436d-a7cb-cfce88a73e11"
      }
    ]
  },
  "27672211": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/27672211.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the Dre2 protein from Escherichia coli, as indicated by the detailed methods for protein expression and purification using a His₆ tag and Ni-NTA affinity columns. Additionally, the paper mentions the use of site-directed mutagenesis to create specific mutants of the Dre2 protein, which is a common practice in enzymology to study the function of specific residues. The paper also describes the use of Electron Paramagnetic Resonance (EPR) spectroscopy to analyze the Fe/S clusters in the Dre2 protein, which is relevant to understanding the enzymatic activity of the protein. Overall, the focus on protein purification and characterization aligns well with the criteria for an experimental enzymology paper.\n",
        "doc_id": "46724477-eba4-4cc1-8d13-7a2b767bbfc2"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Dre2 protein in E. coli, as indicated by the mention of constructing various Cys to Ala mutants and the subsequent analysis of these recombinant proteins. The paper also describes the use of EPR (Electron Paramagnetic Resonance) spectroscopy to analyze the iron-sulfur clusters in the Dre2 protein, which is a method often employed in enzymology to study the properties and activities of enzymes. The focus on the structural and functional analysis of the enzyme through these methods aligns well with the characteristics of experimental enzymology papers.\n",
        "doc_id": "860e8138-5161-446d-9ba2-10a2b72b7a36"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text mentions the expression and purification of the recombinant yeast C116A Dre2 protein in Escherichia coli, which indicates that the authors are working with a specific enzyme. Additionally, the paper discusses the use of EPR (Electron Paramagnetic Resonance) spectroscopy to analyze the properties of the enzyme and its mutants, which is a common method in enzymology to study enzyme activity and structure. The focus on specific amino acid mutations and their effects on the enzyme's properties further supports the classification of this paper as an experimental enzymology study.\n",
        "doc_id": "21f68975-5eb8-421b-ab34-61d76064a5ba"
      },
      {
        "page": 5,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the Dre2 protein and its variants from Escherichia coli, as well as the investigation of iron-sulfur clusters using EPR spectroscopy. The mention of cloning, expressing, and purifying human anamorsin, along with the analysis of its EPR spectra, indicates that the authors are studying the enzymatic properties and characteristics of these proteins, which is a key aspect of experimental enzymology. The focus on the ligation of iron-sulfur clusters and the effects of chemical reconstitution further supports its classification as an experimental enzymology paper.\n",
        "doc_id": "a22002f7-725d-445a-88fd-46075fcde379"
      },
      {
        "page": 6,
        "text": "\nYes: this paper is a good example of an enzymology paper. The text discusses the overexpression and purification of the Dre2 protein, including specific methods used for purification in an anaerobic chamber, which is a common practice in experimental enzymology to maintain the integrity of sensitive cofactors. Additionally, the paper describes experiments involving the reconstitution of the protein with iron and sulfide, and the subsequent analysis of the protein's spectral properties, which suggests an investigation into the enzymatic activity and function of the purified enzyme. The mention of using plasmids for expression and the analysis of mutant forms further indicates a focus on enzymatic properties and functionality, characteristic of experimental enzymology studies.\n",
        "doc_id": "522e7bba-5d6e-4a04-8fc8-14847e42e89f"
      }
    ]
  },
  "8692863": {
    "Path": "/data/ralmadamonter/llm_project/pdfs/SAMs/8692863.pdf",
    "Format": "pdf",
    "pages": [
      {
        "page": 1,
        "text": "Yes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the TcmN polyketide cyclase enzyme from Streptomyces glaucescens, as well as the methods used for its purification and reconstitution. The paper also describes the enzymatic activity of the purified enzyme, specifically how the addition of purified TcmN enhances the production of the polyketide Tcm F2, indicating that an in vitro enzymatic assay was performed to measure the activity of the enzyme. The detailed methods section outlines the purification process and the assays conducted, which are characteristic of experimental enzymology studies.\n",
        "doc_id": "36c23212-78e4-4a6b-8585-642bb30d6104"
      },
      {
        "page": 2,
        "text": "\nYes: this paper is a good example of an enzymology paper. It discusses the overexpression and purification of the TcmN protein, detailing the methods used for purification such as gel filtration and anion exchange chromatography. The paper also includes an in vitro enzymatic assay to measure the O-methyltransferase activity of the purified TcmN enzyme, indicating that the authors conducted experiments to assess the enzyme's functionality. The presence of specific details about the purification process and the enzymatic assays confirms that this paper fits the criteria for an experimental enzymology paper.\n",
        "doc_id": "6b906e9d-fcf6-4097-973b-54f00ec84a17"
      },
      {
        "page": 3,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of the TcmN enzyme, as indicated by the mention of \"overexpression of the tcmN gene\" and the purification steps outlined in the text, including cell-free extracts and various chromatography techniques (e.g., Sephacryl S-200, Mono Q HR). Additionally, the paper describes an in vitro enzymatic assay to measure the activity of the purified enzyme, specifically noting the formation of Tcm B3 and defining one unit of TcmN activity. This focus on enzyme purification and activity measurement is characteristic of experimental enzymology studies.\n",
        "doc_id": "ad7bfaa0-0aee-49db-916f-ab70af4a4718"
      },
      {
        "page": 4,
        "text": "\nYes: this paper is a good example of an experimental enzymology paper. It discusses the overexpression and purification of proteins related to type II polyketide synthases (PKS), specifically mentioning the purification of TcmN and its role in enzymatic assays. The paper describes in vitro assays to measure the thioesterase activity of TcmN, including details about the incubation conditions, the components of the assay (such as acetyl-CoA and malonyl-CoA), and the methods used to analyze the results (like HPLC). The focus on enzyme activity and the experimental setup for measuring this activity clearly aligns with the characteristics of experimental enzymology.\n",
        "doc_id": "19b536da-41ea-48dd-9b14-1bb9691bc9d3"
      }
    ]
  }
}