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The dataset generation failed
Error code: DatasetGenerationError
Exception: CastError
Message: Couldn't cast
id: string
category: string
instruction: string
input: string
output: string
metadata: struct<source_file: string, type: string, source: string, task: string, cell_type: string, tissue: s (... 1743 chars omitted)
child 0, source_file: string
child 1, type: string
child 2, source: string
child 3, task: string
child 4, cell_type: string
child 5, tissue: string
child 6, disease: string
child 7, organism: string
child 8, assay: string
child 9, split: string
child 10, generation_method: string
child 11, top_genes: list<item: string>
child 0, item: string
child 12, canonical_smiles: string
child 13, compound_name: null
child 14, pubchem_cid: null
child 15, MW: double
child 16, LogP: double
child 17, TPSA: double
child 18, QED: double
child 19, functional_groups: list<item: string>
child 0, item: string
child 20, moleculenet_labels: struct<label: double, NR-AR: double, NR-AR-LBD: double, NR-AhR: double, NR-Aromatase: double, NR-ER: (... 1250 chars omitted)
child 0, label: double
child 1, NR-AR: double
child 2, NR-AR-LBD: double
child 3, NR-AhR: double
child 4, NR-Aromatase: double
child 5, NR-ER: double
child 6, NR-ER-LBD: double
child 7, NR-PPAR-gamma: double
child 8, SR-ARE: double
child 9, SR-ATAD5: double
child 10, SR-HSE: double
child 11, SR-MMP: double
child 12, SR-p53: double
child 13, FDA_APPROVED: int64
child 14, CT_TOX: int64
...
d 18, Eye disorders: int64
child 19, Investigations: int64
child 20, Musculoskeletal and connective tissue disorders: int64
child 21, Gastrointestinal disorders: int64
child 22, Social circumstances: int64
child 23, Immune system disorders: int64
child 24, Reproductive system and breast disorders: int64
child 25, Neoplasms benign, malignant and unspecified (incl cysts and polyps): int64
child 26, General disorders and administration site conditions: int64
child 27, Endocrine disorders: int64
child 28, Surgical and medical procedures: int64
child 29, Vascular disorders: int64
child 30, Blood and lymphatic system disorders: int64
child 31, Skin and subcutaneous tissue disorders: int64
child 32, Congenital, familial and genetic disorders: int64
child 33, Infections and infestations: int64
child 34, Respiratory, thoracic and mediastinal disorders: int64
child 35, Psychiatric disorders: int64
child 36, Renal and urinary disorders: int64
child 37, Pregnancy, puerperium and perinatal conditions: int64
child 38, Ear and labyrinth disorders: int64
child 39, Cardiac disorders: int64
child 40, Nervous system disorders: int64
child 41, Injury, poisoning and procedural complications: int64
child 21, name: null
child 22, cid: null
child 23, target: string
child 24, has_evidence: bool
child 25, fgs: list<item: string>
child 0, item: string
to
{'instruction': Value('string'), 'input': Value('string'), 'output': Value('string')}
because column names don't match
Traceback: Traceback (most recent call last):
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1779, in _prepare_split_single
for key, table in generator:
^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 299, in _generate_tables
self._cast_table(pa_table, json_field_paths=json_field_paths),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/json/json.py", line 128, in _cast_table
pa_table = table_cast(pa_table, self.info.features.arrow_schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2321, in table_cast
return cast_table_to_schema(table, schema)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/table.py", line 2249, in cast_table_to_schema
raise CastError(
datasets.table.CastError: Couldn't cast
id: string
category: string
instruction: string
input: string
output: string
metadata: struct<source_file: string, type: string, source: string, task: string, cell_type: string, tissue: s (... 1743 chars omitted)
child 0, source_file: string
child 1, type: string
child 2, source: string
child 3, task: string
child 4, cell_type: string
child 5, tissue: string
child 6, disease: string
child 7, organism: string
child 8, assay: string
child 9, split: string
child 10, generation_method: string
child 11, top_genes: list<item: string>
child 0, item: string
child 12, canonical_smiles: string
child 13, compound_name: null
child 14, pubchem_cid: null
child 15, MW: double
child 16, LogP: double
child 17, TPSA: double
child 18, QED: double
child 19, functional_groups: list<item: string>
child 0, item: string
child 20, moleculenet_labels: struct<label: double, NR-AR: double, NR-AR-LBD: double, NR-AhR: double, NR-Aromatase: double, NR-ER: (... 1250 chars omitted)
child 0, label: double
child 1, NR-AR: double
child 2, NR-AR-LBD: double
child 3, NR-AhR: double
child 4, NR-Aromatase: double
child 5, NR-ER: double
child 6, NR-ER-LBD: double
child 7, NR-PPAR-gamma: double
child 8, SR-ARE: double
child 9, SR-ATAD5: double
child 10, SR-HSE: double
child 11, SR-MMP: double
child 12, SR-p53: double
child 13, FDA_APPROVED: int64
child 14, CT_TOX: int64
...
d 18, Eye disorders: int64
child 19, Investigations: int64
child 20, Musculoskeletal and connective tissue disorders: int64
child 21, Gastrointestinal disorders: int64
child 22, Social circumstances: int64
child 23, Immune system disorders: int64
child 24, Reproductive system and breast disorders: int64
child 25, Neoplasms benign, malignant and unspecified (incl cysts and polyps): int64
child 26, General disorders and administration site conditions: int64
child 27, Endocrine disorders: int64
child 28, Surgical and medical procedures: int64
child 29, Vascular disorders: int64
child 30, Blood and lymphatic system disorders: int64
child 31, Skin and subcutaneous tissue disorders: int64
child 32, Congenital, familial and genetic disorders: int64
child 33, Infections and infestations: int64
child 34, Respiratory, thoracic and mediastinal disorders: int64
child 35, Psychiatric disorders: int64
child 36, Renal and urinary disorders: int64
child 37, Pregnancy, puerperium and perinatal conditions: int64
child 38, Ear and labyrinth disorders: int64
child 39, Cardiac disorders: int64
child 40, Nervous system disorders: int64
child 41, Injury, poisoning and procedural complications: int64
child 21, name: null
child 22, cid: null
child 23, target: string
child 24, has_evidence: bool
child 25, fgs: list<item: string>
child 0, item: string
to
{'instruction': Value('string'), 'input': Value('string'), 'output': Value('string')}
because column names don't match
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1348, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 980, in convert_to_parquet
builder.download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 882, in download_and_prepare
self._download_and_prepare(
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 943, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1646, in _prepare_split
for job_id, done, content in self._prepare_split_single(
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/builder.py", line 1832, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
instruction string | input string | output string |
|---|---|---|
Describe the effect of mutation P69391-I45K on protein Alpha-pompilidotoxin. | ### Wild-type:
MFKQLILLALAAVFLLINISSAEPAAEPNANAEPLAEASAEPRIIIGLFDQLSKLG
### Mutant:
MFKQLILLALAAVFLLINISSAEPAAEPNANAEPLAEASAEPRIKIGLFDQLSKLG
### Answer: | Complete gain of potency; when associated with K-442. |
Determine whether these two protein sequences are homologous. | ### Sequence 1:
MPAPTKRERQNRKRFERNRSVRTRLRNLSKKFYRALDAGDLESARSVRDEAQKAYDKAAGKGIIHRNKASRKLSRFDRALAGRG
### Sequence 2:
SAIKRHKQSVKRAARNRAVKTRIKNAIKAVRTAVTEKDKEQAQAKLTDAMSVLDKASSKGVIHWKNAARKISRLSKAVDG
### Answer: | Homologous |
Which tissue is this cell most likely from? | MRC1, CD163, CD68, C1QA, C1QB | This profile is most consistent with macrophage, which is commonly found in lung under typical physiological conditions. |
Describe the effect of mutation P41180-L11S on protein Extracellular calcium-sensing receptor. | ### Wild-type:
MAFYSCCWVLLALTWHTSAYGPDQRAQKKGDIILGGLFPIHFGVAAKDQDLKSRPESVECIRYNFRGFRWLQAMIFAIEEINSSPALLPNLTLGYRIFDTCNTVSKALEATLSFVAQNKIDSLNLDEFCNCSEHIPSTIAVVGATGSGVSTAVANLLGLFYIPQVSYASSSRLLSNKNQFKSFLRTIPNDEHQATAMADIIEYFRWNWVGTIAADDDYGRPGIEKFREEAEERDICIDFSELISQYSDEEEIQHVVEVIQNSTAKVIVVFSSGPDLEPLIKEIVRRNITGKIWLASEAWA
###... | In HHC1; demonstrates reduced intracellular and plasma membrane expression and signaling to the MAPK pathway in response to extracellular calcium relative to wild-type; fails to be inserted in the microsomes and does not undergo proper glycosylation. The mutation in the CASR gene leads to reduced intracellular and plas... |
Based on the top expressed genes, infer the cell type. | <cell>
LST1 CDKN1C MS4A7 FCGR3A
</cell> | This cell is most consistent with CD16+ monocyte, a non-classical CD16+ monocyte. Key markers such as CDKN1C, MS4A7, FCGR3A support this identity. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MKTSMFLTLTGLVLLFVVCYASESEEKEFPKELLSSIFAADSDFKVEERGCLGDKCDYNNGCCSGYVCSRTWKWCVLAGPWCR
### Sequence 2:
MSIKPLHDRIVVKPIEADEVSPGGIVIPDSAKEKSTKGEVIAVGTGKPLDNGNVRTPSIKVGDKVIYGQYAGSTYKAEGVEYKVLREDDILAIIG
### Answer: | Non-Homologous |
Determine whether these two protein sequences are homologous. | ### Sequence 1:
MKGYLWGGASVVLVTVAQLVLKWGMMNIPLLSLADINVQFLTMYFVQLASVMCGLMGYALSMLCWFFALRYLPLNRAYPLLSLSYALVYLGAVLLPWFNEPATLLKTLGAGFILLGIWLINIKPIKAS
### Sequence 2:
MPLPPDITFDSLALIKMHSQSMKKILEITLAKFTVNLSIVTVYRYLTVRAYLKKNIELELDVLKDIYNIVPLNEEIAIKAAQIEADLMRKGMMPDIEDVLTAATAIYTKSLLITDDSKRYEPMRRFGLDTMPLDKFVKEVELMVEKELI
### Ans... | Non-Homologous |
Analyze the molecular properties of the given SMILES. | CCc1cc([C@]2(c3cccc(-c4cncnc4)c3)N=C(N)N(C)C2=O)ccn1 | This molecule is medium-sized and polar, with moderately lipophilic character. It contains aromatic ring, amide, amine, pyridine. Its descriptor profile: MW=372.43, LogP=2.13, TPSA=97.36, HBD=1, HBA=6, QED=0.76. |
Given the expression strengths of marker genes, what cell type is this? | <cell>
GNLY:medium FCGR3A:medium KLRD1:low
</cell> | This cell is most consistent with natural killer cell, a natural killer (NK) cell. Key markers such as KLRD1, FCGR3A, GNLY support this identity. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MESPLGSDLARLVRVWRALIDHRLKPLELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCSSDRRAKRIKLTEKAEPLINEMEEVIGKTRDEILSGVSKQEVETLLHLIRKLEQNILDLQAKD
### Sequence 2:
MESPLGSDLARLVRIWRALIDHRLKPLELTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEMEAVINKTRAEILHGISAEELEQLITLIAKLEHNIIELQA... | Homologous |
Analyze the molecular properties of the given SMILES. | Cn1c2ccccc2c2cc(-c3ccccc3)c3c(c21)C(=O)c1ccccc1C3=O | This molecule is medium-sized and relatively nonpolar, with lipophilic character. It contains aromatic ring, ketone. Its descriptor profile: MW=387.44, LogP=5.77, TPSA=39.07, HBD=0, HBA=2, QED=0.36. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MANRLKEKYLNEVVPALTEQFNYSSVMAVPKVDKIVLNMGVGDAVSNAKNLEKAAQELALISGQKPLITKAKKSIAGFRLREGVAIGAKVTLRGERMYEFLDKLVTVSLPRVRDFHGVPTKSFDGRGNYTLGVKEQLIFPEINFDDVDKTRGMDIVIVTTANTDEESRALLTGLGMPFAK
### Sequence 2:
MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQREHVLPVVALCTVSDIVLIAAGIAGFGALIGAHPRALNVVKFGGAAFLIGYGLLAARRAWRPVALIPSGATPVR... | Non-Homologous |
Describe the cell state from this top-gene list. | <cell>
IRF7 TCF4 CLEC4C GZMB
</cell> | This cell is most consistent with plasmacytoid dendritic cell, a plasmacytoid dendritic cell (pDC). Key markers such as CLEC4C, IRF7, GZMB support this identity. |
What is the function of this protein? | ### Protein Sequence:
GCSP_XANAC
### Answer: | The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. |
Describe the effect of mutation P51159-P70L on protein Ras-related protein Rab-27A. | ### Wild-type:
MSDGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKFITTVGIDFREKRVVYRASGPDGATGRGQRIHPQLWDTAGQERFRSLTTAFFRDAMGFLLLFDLTNEQSFLNVRNWISQLQMHAYCENPDIVLCGNKSDLEDQRVVKEEEAIALAEKYGIPYFETSAANGTNISQAIEMLLDLIMKRMERCVDKSWIPEGVVRSNGHASTDQLSEEKEKGACGC
### Mutant:
MSDGDYDYLIKFLALGDSGVGKTSVLYQYTDGKFNSKFITTVGIDFREKRVVYRASGPDGATGRGQRIHL... | Enables interaction with SYTL2. |
Describe the effect of mutation P27838-K31D on protein Iron-sulfur cluster assembly protein CyaY. | ### Wild-type:
MNDSEFHRLADQLWLTIEERLDDWDGDSDIKCEINGGVLTITFENGSKIIINRQEPLHQVWLATKQGGYHFDLKGDEWICDRSGETFWDLLEQAATQQAGETVSFR
### Mutant:
MNDSEFHRLADQLWLTIEERLDDWDGDSDIDCEINGGVLTITFENGSKIIINRQEPLHQVWLATKQGGYHFDLKGDEWICDRSGETFWDLLEQAATQQAGETVSFR
### Answer: | Decreases kinetics of Fe-S formation on IscU. |
Predict the Foldseek 3Di structural alphabet sequence for the amino-acid sequence below. | ### Sequence 1D:
HFSIPETESRAYVAYNIHVNGVLHCRVRYSQLLGLHEQLRKEYGANVLPAFPPKKLFSLTPAEVEQRREQLEKYMQAVRQDPLLGSSETFNSFLRRAQQEAH
### Answer: | <SEQ_3Di>DWAWDDWDCDPFIKTFIDDPPHTFFIGGPVVVVVLVVVCCVVPNPPPADDQDDDDDDDDDPVRVVVNRVRVRVRVVSQCVDPDRVPDVSVVVVSVVRRVVRD</SEQ_3Di> |
Determine whether these two protein sequences are homologous. | ### Sequence 1:
MTPYIVILSTGSELTAGRSVDTNSGWIANQLFELGWKVKKIITLPDDPNLIFKELEALQSLAKEIPVLAIMTGGLGPTEDDYTLETVLKLTGKTSYAVEKAKIRLTKIYEARGKDYKDILPTVFRQTNVPEGCKTLDNSVGIAVGFIESLGENSYLVCMPGVPSEMTEMFKRRLVPELKKMYPRENLIQKTKWLWNIGESLFQNEFIEPNREVYFKETEWGVTANRGYIKCIFQSTNDVMLDTILKSLEKQYPDLISDDVFQYVHEQLLYEKWTISVVESCTGGLLGKKLTERAGSSAYFMGGF... | Homologous |
Predict the secondary-structure string for the amino-acid sequence below. Use DSSP-style symbols. | ### Sequence 1D:
MGVFTFEDEITSTVPPAKLYNAMKDADSITPKIIDDVKSVEIVEGNGGPGTIKKLTIVEDGETKFILHKVESIDEANYAYNYSVVGGVALPPTAEKITFETKLVEGPNGGSIGKLTLKYHTKGDAKPDEEELKKGKAKGEGLFRAIEGYVLANPTQY
### Answer: | <SEQ_2D>CCEEEEEEEEEESSCHHHHHHHHHTHHHHHHHHCTTEEEEEEEESCSSTTCEEEEEEEETTEEEEEEEEEEECCTTTTEEEEEEEEETTSCTTEEEEEEEEEEEEEGGGEEEEEEEEEEEESTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHCGGGC</SEQ_2D> |
Predict the Foldseek 3Di structural alphabet sequence for the amino-acid sequence below. | ### Sequence 1D:
APIPGVMPIGNYVSLYVMLPLGVVNADNVFPDKEKVEDELKQVKAGGCDGVMVDVWWGIIEAKGPKQYDWSAYRELFQLVKKCGLKIQAIMSFHQCGGNVGDAVFIPIPQWILQIGDKNPDIFYTNRAGNRNQEYLSLGVDNQRLFQGRTALEMYRDFMESFRDNMADFLKAGDIVDIEVGCGAAGELRYPSYPETQGWVFPGIGEFQCYDKYMVADWKEAVKQAGNADWEMPGKGAGTYNDTPDKTEFFRPNGTYKTDMGKFFLTWYSNKLIIHGDQVLEEANKVFVGLRVNIAAKVSGIHW... | <SEQ_3Di>DFDPPDFFQLLFFAEEFEEDPPCQALQRARPPVVVVLVLLLVCVVLQHAAYEYEPAQLRAQAPHQPRGDCVSVVVVLVSNVVSVHAYEYEDQQWWDDDDPPDPGTRFHHVLVVVLCVVPVLQAFAFPVGDGDRGHGDLLQQPPLRRVRRTVLVSLLVVLLVVCVVCVVCLVVQRYFEYAYQQEYVSALWYCFQPVVVPADPPFLGGARQPRPSSVVVVLVVVVVVVHNPLDDDDCQLPHGRDDQCPHQQRNDPHVCPDPSNVSVLLSQLVSSLVSVLSNLLSVLVNQFQTQHAYEHEHEQNFFCPQPQRSS... |
Identify the compound name from the given SMILES. | Oc1ccccc1-c1nnco1 | The SMILES represents an unnamed molecule with MW=162.15, LogP=1.44, TPSA=59.15. PubChem lookup would be required to retrieve a canonical compound name or synonyms. |
What is the protein family that this protein belongs to? | ### Protein Sequence:
RS4_DEHMC
### Answer: | Belongs to the universal ribosomal protein uS4 family. |
Describe the effect of mutation P36163-A332C on protein Mitochondrial metalloendopeptidase OMA1. | ### Wild-type:
MLRNIIRFKGFGKGTSGGFLKPVSFRVQLTRCYRYDNGPSYRRFNNGEYSQKSSFKSILLDKSSRKYLALLFGGCSLFYYTHLDKAPVSDRSRFIWVSRPLELTIGNYTYKSIWRQTQQEILPPQHPLSIKIENIFMKIVEAAYKDPSVDNSLLDGIKWEIHVVNDPTASPNAFVLPGGKVFIFSSILPICANDDGIATVLAHEFAHQLARHTAENLSKAPIYSLLGLVLYTVTGAHAINNILLDGFLRMPASRQMETEADYIGLMIMSRACFQPQESIKVWERMANFEKQMNRGGVVNM
###... | Impaired disulfide bond, leading to abolished conformational state; when associated with A-272. The study suggests that the disulfide bond formed by C332 is also involved in the deregulation of Oma1 function. |
Based on the marker genes, describe the enriched biological pathway. | PDGFRB, S100A4, ACTA2, FAP, COL1A1 | The marker profile is enriched for extracellular matrix organization, consistent with cancer-associated fibroblast function. |
Predict the secondary-structure string for the amino-acid sequence below. Use DSSP-style symbols. | ### Sequence 1D:
PRSLANAPIMILNGPNLNLLGQRQPEIYGSDTLADVEALCVKAAAAHGGTVDFRQSNHEGELVDWIHEARLNHCGIVINPAAYSHTSVAILDALNTCDGLPVVEVHISNIHQREPFRHHSYVSQRADGVVAGCGVQGYVFGVERIAALAGAGSARA
### Answer: | <SEQ_2D>CCCTTTSCEEEEECTTGGGBTTBCHHHHCSCCHHHHHHHHHHHHHTTTCCEEEEECSCHHHHHHHHHHHHHHCSEEEEECGGGGGTCHHHHHHHHTCTTSCEEEEESSCGGGSCGGGGCCSGGGTCSCEEESSTTHHHHHHHHHHHHHHHCCCCCC</SEQ_2D> |
What is the protein family that this protein belongs to? | ### Protein Sequence:
ENGB_ANAPZ
### Answer: | Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. EngB GTPase family. |
Identify the cell type from the given marker gene expression profile. | <cell>
RBFOX3:high SLC17A7:high SATB2:high
</cell> | This cell is most consistent with excitatory neuron, an excitatory (glutamatergic) neuron. Key markers such as RBFOX3, SATB2, SLC17A7 support this identity. |
Predict the Foldseek 3Di structural alphabet sequence for the amino-acid sequence below. | ### Sequence 1D:
QRANIDFERKGSLTLHKKKGAAGEPLNGVTFKITKLNFDLQNGDWAKFPKTAADAKGHETSTTKEVETSGNGTAVFDNLDLGIYLVEETKAPDGIVTGAPFIVSIPMVNEASDAWNYNVVAYPKNTETKTEKTVKDADQNIQDAYTYTIKADAPTWKKLTAFRFEDELDKRLDFQKVTEVKAGDTVLGTSDYTVNDPATDGNKLVVTLTDEGLKKVKSGDKMSLTFEVKRKEVGNTTELKNRADVIFNNPNTDKEVKNKTNEVVTYHGKLKVVKKDGKEAGKVLKGAEFELYQCTSAAVLGKG... | <SEQ_3Di>DDLDDDQVDFFKEKEQEAEDVVHQGFWFWKKKKFFFQDDPPPGDPVQDDFFPVSRPPGTDPDMDMFTQDDSNMTMDTRHRFGKIKMDTDDGDAQKQFAAIGMDGQFDDPDPPDRTHRYHYDYGYIYGKDKAKWWACPFNAAQRKTKIKIKIWDAADLFWDKKKKKKQFDPQKDFDWWDFKDFAPDTDDPVQWDWDHCVPVVNMTMIMGDPVNRVPHDGGTTIMTMTMMGRNFCPPHQKGKIKMKMWTQRSNYRDIHIDIYDIFIWGKFKEKEWEDAPPDPPHTDWFWKKFKFKALDQVGTDDDSDQQPNDG... |
Predict the secondary-structure string for the amino-acid sequence below. Use DSSP-style symbols. | ### Sequence 1D:
MEAAASEPSLDLDNLKLLELIGRGRYGAVYKGSLDERPVAVKVFSFANRQNFINEKNIYRVPLMEHDNIARFIVGDERVTADGRMEYLLVMEYYPNGSLCKYLSLHTSDWVSSCRLAHSVTRGLAYLHTELPRGDHYKPAISHRDLNSRNVLVKNDGTCVISDFGLSMRLTGNRLVRPGEEDNAAISEVGTIRYMAPEVLEGAVNLRDCESALKQVDMYALGLIYWEIFMRCTDLFPGESVPEYQMAFQTEVGNHPTFEDMQVLVSREKQRPKFPEAWKENSLAVRSLKETIEDCWDQDAEAR... | <SEQ_2D>CCCCCCCCCCCCSSCEEEEEEEECSSCEEEEEEETTEEEEEEEEEGGGHHHHHHHHHHHHSTTCCCTTBCCEEEEEEEECTTSCEEEEEEECCCTTCBHHHHHHHCCBCHHHHHHHHHHHHHHHHHHHCCCCSSSSCCCCEECSSCSGGGEEECTTSCEEECCCTTCEECSCCCCCCCCCCCCCCCCCCSCGGGCCHHHHHTCCCGGGHHHHHHHHHHHHHHHHHHHHHTTBGGGSTTSCCCCCCCTTHHHHCSSCCHHHHHHHHTTTCCCCCCCTTSCTTSHHHHHHHHHHHHHSCSSGGGSCCHHHHHHH... |
Which functional groups are present in this SMILES? | CCN(C(=O)Cc1ccc(S(C)(=O)=O)cc1)C1CCN(CCC(c2ccc(NC(C)=O)cc2)c2cccc(F)c2)CC1 | The molecule contains the following functional groups: aromatic ring, amide, amine, halide. |
What are the official names of this protein? | ### Protein Sequence:
LEU1_ENT38
### Answer: | 2-isopropylmalate synthase, Alpha-IPM synthase, Alpha-isopropylmalate synthase. |
Predict the secondary-structure string for the amino-acid sequence below. Use DSSP-style symbols. | ### Sequence 1D:
MTTAGVSRRPGRLAGKAAIVTGAAGGIGRATVEAYLREGASVVAMDLAPRLAATRYEEPGAIPIACDLADRAAIDAAMADAVARLGGLDILVAGGALKGGTGNFLDLSDADWDRYVDVNMTGTFLTCRAGARAMVAAGAGKDGRSARIITIGSVNSFMAEPEAAAYVAAKGGVAMLTRAMAVDLARHGILVNMIAPGPVDVTGNNTGYSEPRLAEQVLDEVALGRPGLPEEVATAAVFLAEDGSSFITGSTITIDGGLSAMIFGGMREGRR
### Answer: | <SEQ_2D>CCCCCCCCCCCTTTTCEEEEESCSSHHHHHHHHHHHHTTCEEEEEECHHHHHTCCCSSSCCEEEECCCCCHHHHHHHHHHHHHHHTSCSEEEECCCCCCCCSCGGGCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSCCEEEEEECCGGGTSCCTTCHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEECSBCCSSSSCTTCSHHHHHHHHHHCTTSSCBCHHHHHHHHHHHHSGGGTTCCSCEEEESTTGGGCSSGGGSTTTC</SEQ_2D> |
Based on the marker genes, describe the enriched biological pathway. | CD3D, CD4, S100A4, IL7R, CD45RO | The marker profile suggests functional enrichment consistent with the typical biology of memory CD4+ T cell. |
Based on the marker genes, describe the enriched biological pathway. | SLC32A1, GAD2, GAD1 | The marker profile is enriched for synaptic signaling and neurotransmission, consistent with inhibitory neuron function. |
Judge if the following two protein sequences share an evolutionary origin. | ### Sequence 1:
MSLLDMGGDMMEDDWEFASSSNPKRTLVLVGRTGNGKSATGNSILGRKAFRSRARTVGVTSTCESQRVVQEDGDIINVVDTPGLFDLSTAADFIGKEIVRCISLAEDGIHAILLVFSVRRLAEEEQTVLSFLQALFGSKIADYMIVVFTGGDELEENEETLEEYLADYCPEFLKEILGICDNRLVLFNNKTTDKVKKAEQVQKLLSLVESVVKQNNGKPYSDELFHELQEEAIKLRDQKKEVELLQGYSNNEIDEFKKQIDMSYDRQLSRITEMVETKLRDTAKRLEQQLGEEQAARLEAEKRA... | Non-Homologous |
Describe the effect of mutation O04331-N165D on protein Prohibitin-3, mitochondrial. | ### Wild-type:
MGSQQAAVSFLSNLAKAAFGLGTAATVLNTSLFTVDGGERAVIFDRFRGVMDQTVGEGTHFLIPILQRPHIFDIRTKPHTFSSISGTKDLQMVNLTLRVLSRPEVSRLPYIFQTLGLEYDEKVLPSIGNEVLKAVVAQFNADQLLTERPHVSALVRESLITRAKNFNIVLDDVAITHLSYGVEFSRAVEQKQVAQQEAERSKFVVMKADQERRAAVIRAEGESEAAQLISDATAKAGMGLIELRRIEASREIASTLARSPNVAYLPGGQSMLFALNR
### Mutant:
MGSQQAAVSFLSNL... | Decreased sensitivity and minimal response to ethylene, as well as decreased ethylene production. The eer3-1 mutation represents a conditional allele with an ethylene-independent phenotype that results from an amino acid substitution in the previously uncharacterized prohibitin, AtPHB3, with complete gain of EER3 funct... |
Classify the pair below as homologous or non-homologous. | ### Sequence 1:
MKILVTAFDPFGGENINPSYEVLKNLKDNIEGAEIIKIQVPTVFYLSVEKVIEKIKEVKPDAVLSIGQAGGRYDITVERIAINIDDARIPDNIGQQPIDTPIDPEGAPAYFATIPIKEIVEEIKKENIPASISNTAGTFVCNHLMYGILNYVHKNGLNIKAGFIHIPYLPVQVLNKPYTPSMSLGDMVKAIETAIKVIAKKSR
### Sequence 2:
MLRSLVQNPRVRARVLERVDEFRLNNLSNEEVWFRELTLCLLTANSSFISAYQALNCLGDKIYYANEEVIRSILKSCKYRFYN... | Non-Homologous |
What are the official names of this protein? | ### Protein Sequence:
HIC1_HUMAN
### Answer: | Hypermethylated in cancer 1 protein, Hic-1, Zinc finger and BTB domain-containing protein 29. |
Judge if the following two protein sequences share an evolutionary origin. | ### Sequence 1:
MSEKPEKIVLASGNAGKLKEFGNLFEPYGITVLPQSEFSIPECPEPYSTFVENALAKARHAAGHSGLPALADDSGICAAALNGAPGIHSARYAGSNPKSDTANNLKLAAELAGKADKSCCYVCVLVFVRHKDDPRPIIAEGVWHGQWNGVPAGENGFGYDPYFYLPGHGKTAAELDSEVKNRESHRAQALAELLRKLAL
### Sequence 2:
MKLMDVHVLFSGGKDSSLSAVILKKLGYNPHLITINFGVIPSYKLAEETAKILGFKHKVITLDRKIVEKAADMIIEHKYPGPAIQYV... | Non-Homologous |
What is the protein family that this protein belongs to? | ### Protein Sequence:
OBG1_ANAMF
### Answer: | Belongs to the TRAFAC class OBG-HflX-like GTPase superfamily. OBG GTPase family. |
Judge if the following two protein sequences share an evolutionary origin. | ### Sequence 1:
MRCLPVFVILLLLIASTPSDTVPLKTKDDMPQASFHGNARRTLQMLSKKQCCWYFDISCCITV
### Sequence 2:
MRCLPVFVILLLLIASTPSIDARPKTKDDMPLASFNDNAKRILQILSRKPCCSIHDNSCC
### Answer: | Homologous |
Describe the effect of mutation Q9JHF9-F126A on protein Lymphocyte antigen 96. | ### Wild-type:
MLPFILFSTLLSPILTESEKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNLFISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILFPKGHYRCVAEAIAGDTEEKLFCLNFTIIHRRDVN
### Mutant:
MLPFILFSTLLSPILTESEKQQWFCNSSDAIISYSYCDHLKFPISISSEPCIRLRGTNGFVHVEFIPRGNLKYLYFNLFISVNSIELPKRKEVLCHGHDDDYSFCRALKGETVNTSIPFSFEGILAPKGHY... | Abolishes dimerization of the TLR4 complex and stimulation of TNF production in response to bacterial lipopolysaccharide. The document mentions that MPL was impaired in induction of CD14-dependent TLR4/MD-2 dimerization compared with lipid A. Impaired TLR4/MD-2 dimerization decreased CD14-mediated TNFα production. |
What is the protein family that this protein belongs to? | ### Protein Sequence:
PPAC_DICDI
### Answer: | Belongs to the low molecular weight phosphotyrosine protein phosphatase family. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MKQGTVKWFNAEKGFGFIEVEGENDVFVHFSAINQEGYKSLEEGQSVEFEVVEGDRGPQAANVVKL
### Sequence 2:
MKQGTVKWFNAEKGFGFIEVEGENDVFVHFSAINQEGYKSLEEGQSVEFEVVEGDRGPQAANVVKL
### Answer: | Homologous |
Based on the evidence, describe the ligand-target relationship. | Target: CDK2
Ligand SMILES: CC1CC2C3CCC4=CC(=O)C=CC4(C)C3(F)C(O)CC2(C)C1(O)C(=O)CO
Evidence: No specific activity evidence is provided; the question is a general relationship inference. | Without supporting bioactivity evidence, the relationship between this ligand and cyclin-dependent kinase 2 (CDK2) is best described as an uncharacterized or putative association rather than a confirmed binding claim. |
Describe the effect of mutation Q07794-D288N on protein Histone acetyltransferase RTT109. | ### Wild-type:
MSLNDFLSSVLPVSEQFEYLSLQSIPLETHAVVTPNKDDKRVPKSTIKTQHFFSLFHQGKVFFSLEVYVYVTLWDEADAERLIFVSKADTNGYCNTRVSVRDITKIILEFILSIDPNYYLQKVKPAIRSYKKISPELISAASTPARTLRILARRLKQSGSTVLKEIESPRFQQDLYLSFTCPREILTKICLFTRPASQYLFPDSSKNSKKHILNGEELMKWWGFILDRLLIECFQNDTQAKLRIPGEDPARVRSYLRGMKYPLWQVGDIFTSKENSLAVYNIPLFPDDPKARFIHQLAEE
###... | Decreases histone acetylase activity. The mutant revealed a dramatic 1000-fold decrease in k(cat)/K(m) for AcCoA, consistent with a role in AcCoA binding. |
Predict the Foldseek 3Di structural alphabet sequence for the amino-acid sequence below. | ### Sequence 1D:
MVRFLDGHTPAYDLTYNDVFVVPGRSDVASRFDVDLSTVDGSGTTIPVVVANMTAVAGRRMAETVARRGGIVVLPQDLPITAVSETVDFVKSRDLVVDTPVTLSPEDSVSDANALLHKRAHGAAVVVFEGRPIGLVTEANCAGVDRFARVRDIALSDFVTAPVGTDPREVFDLLEHAPIDVAVMTAPDGTLAGVLTRTGAIRAGIYTPAVDAKGRLRIAAAVGINGDVGAKAQALAEAGADLLVIDTAHGHQAKMLDAIKAVASLDLGLPLVAGNVVSAEGTRDLIEAGASIVKVGVGPGAMC... | <SEQ_3Di>DAAAPPPFDDPAFAFLVFKDFFFDDAPDDDLLLFFQDFDFQLQFRHQEEAEQDQLFDDLLNQQVRLLLGYAYAHHAPDDLVRLLVSLVVQQPADSLFDAFAEDEQQDWLLVVLQSRLLDDQQKGFYDDPQAGQAIDHNVQSPPDDRGDGCVVRGDRDAAEDEPPPQLVVVLVSCPPPPGQKYFYAYPVRGGRHIAGNVSSVSNVRGDRRADPVRGRAYAYEYELPDQLLVVLVSNLVSPHQAYEYEDQDQQDPSNLVSLLSNVVVVSVHQYETYEDQALVSLVSNVVSPHQEYEYWHCCDCPDPVCVPPVD... |
Evaluate whether this molecule is compatible with oral-drug-like descriptors. | SMILES: C=C1CCC=C(C)CC[C@@H]2[C@@H]1CC2(C)C
Descriptors: MW=204.36, LogP=4.73, TPSA=0.0, HBD=0, HBA=0 | Descriptors: MW=204.36, LogP=4.73, TPSA=0.0, HBD=0, HBA=0, QED=0.5, Lipinski violations=0. Overall the molecule is broadly compatible with common oral drug-like descriptors, and a moderate QED score suggests mixed drug-likeness. |
What is the protein family that this protein belongs to? | ### Protein Sequence:
CYNS_PROMP
### Answer: | Belongs to the cyanase family. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MLLGTVVTVLSTLPAIAYAMDPESPEHEGMPQLNFANPLTTSQVVWMALILLAFYLLLSKWALPQVSQVVDDRNASIMGDLDSAHLAKAEANAAVEEMNDAIRRANLEGQAEIEKTVSAAKAKAQQEAAEAHARLERQLADAEARIASSRDTAMGALRDVATDTTQALIARLTGQFPAQDTVEQAVGQALAARS
### Sequence 2:
MPQLNF--DYWPNQIFWLLVTLVAIYFLLTRVALPRIGAVLAERRGTITNDLAAAEELKQKAVLAEKAYNEALAKARAEAQAIVAETRAAIQ... | Homologous |
What is the function of this protein? | ### Protein Sequence:
SURE_HAEDU
### Answer: | Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates. |
Predict the Foldseek 3Di structural alphabet sequence for the amino-acid sequence below. | ### Sequence 1D:
IFKVGDTVVYPHHGAALVEAIETRTIKGEQKEYLVLKVAQGDLTVRVPAENAEYVGVRDVVGQEGLDKVFQVLRAPRRYKANLEKLASGDVNKVAEVVRKRMLAKARQILVGELALAESTDDAKAETILDEVLAA
### Answer: | <SEQ_3Di>DADAQAWWADLPLGIFGWHDWFQPADPPRRFGWTWTQRPPVRPIDTHGPVCCVVQPGGHADAVVLVVLLLVLLQDAVVVVVLLVLSVPNRSNSLSNSCSVVSVVVSLQRVQSSVCPNVVDDPPVCSVVVVVSNND</SEQ_3Di> |
Based on the evidence, describe the ligand-target relationship. | Target: HIV protease
Ligand SMILES: NC(=O)Nc1sc(-c2ccc(F)cc2)cc1C(=O)N[C@H]1CCCNC1
Evidence: No specific activity evidence is provided; the question is a general relationship inference. | Without supporting bioactivity evidence, the relationship between this ligand and HIV-1 protease (HIV protease) is best described as an uncharacterized or putative association rather than a confirmed binding claim. |
What is the function of this protein? | ### Protein Sequence:
AMPA_CHESB
### Answer: | Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides. |
Predict the secondary-structure string for the amino-acid sequence below. Use DSSP-style symbols. | ### Sequence 1D:
MKRPVIILLLGIVTMCAMAQTGDKPVDLKEITSGMFYARSAGRGIRSMPDGEHYTEMNRERTAIVRYNYASGKAVDTLFSIERARECPFKQIQNYEVSSTGHHILLFTDMESIYRHSYRAAVYDYDVRRNLVKPLSEHVGKVMIPTFSPDGRMVAFVRDNNIFIKKFDFDTEVQVTTDGQINSVLNGATDWVYEEEFGVTNLMSWSADNAFLAFVRSDESAVPEYRMPMYEDKLYPEDYTYKYPKAGEKNSTVSLHLYNVADRNTKSVSLPIDADGYIPRIAFTDNADELAVMTLNRLQNDFK... | <SEQ_2D>CCCCCCCCCCCCCCCCCCCCCCSBCCCHHHHHTTTTCCCCSCSCCEECTTSSEEEEECTTSSEEEEEETTTCCEEEEEEETTTSBTCCCSCCSEEEECTTSSEEEEEEEEEECSSSCEEEEEEEEETTTTEEEESSSSCSCBEEEEECTTSSEEEEEETTEEEEEETTTTEEEECCSCCBTTTEEESSCCHHHHHHHCCSCCEEECTTSSEEEEEEEECTTSCEEEEEECTTCSSCEEEEEECCBTTSCCCEEEEEEEETTTTEEEEECCSSCTTCEEEEEEECSSTTCEEEEEECTTSCEEEEEEECTTTC... |
What are the official names of this protein? | ### Protein Sequence:
KEFF_SHIB3
### Answer: | Glutathione-regulated potassium-efflux system ancillary protein KefF, Quinone oxidoreductase KefF. |
Describe the effect of mutation Q9SQQ9-K74R on protein Myb-related protein 2. | ### Wild-type:
MYYQNQHQGKNILSSSRMHITSERHPFLRGNSPGDSGLILSTDAKPRLKWTPDLHERFIEAVNQLGGADKATPKTIMKVMGIPGLTLYHLKSHLQKYRLSKNLNGQANNSFNKIGIMTMMEEKTPDADEIQSENLSIGPQPNKNSPIGEALQMQIEVQRRLHEQLEVQRHLQLRIEAQGKYLQSVLEKAQETLGRQNLGAAGIEAAKVQLSELVSKVSAEYPNSSFLEPKELQNLCSQQMQTNYPPDCSLESCLTSSEGTQKNSKMLENNRLGLRTYIGDSTSEQKEIMEEPLFQRMELT
###... | No effect on nuclear localization. No effect nuclear localization; when associated with R-70 and R-78. |
Identify the functional groups in the given SMILES. | CC1(C)C2CCC(N)(C2)C1O.Cl | The molecule contains the following functional groups: amine, hydroxyl, halide. |
Predict the secondary-structure string for the amino-acid sequence below. Use DSSP-style symbols. | ### Sequence 1D:
MGHHHHHHSHMGSEIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYLWRNIIPHVAPSHRCIAPDLIGMGKSDKPDLDYFFDDHVRYLDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIACMEFIRPIPTWDEWPEFARETFQAFRTADVGRELIIDQNAFIEGALPMGVVRPLTEVEMDHYREPFLKPVDREPLWRFPNELPIAGEPANIVALVEAYMNWLHQSPVPKLLFWGTPGVLIPPAEAARLAESLPNCKTVDIGPGLFLLQEDNPDLIGSEIARWLPG... | <SEQ_2D>CCCCCCCCCCCCCCCCCCCCCCCEEEEETTEEEEEEEESCSSSCCEEEECCTTCCGGGGTTTHHHHTTTSCEEEECCTTSTTSCCCSCCCCHHHHHHHHHHHHHHTTCCSEEEEEEEHHHHHHHHHHHHSGGGEEEEEEEEECCCBCSGGGSCGGGHHHHHHHTSTTHHHHHHTTSCHHHHTHHHHTCSSCCCHHHHHHHHGGGSSGGGGHHHHHHHHHSCBTTBSHHHHHHHHHHHHHHHHCCSCEEEEEEEECSSSCHHHHHHHHHHSTTEEEEEEEEECSCHHHHCHHHHHHHHHHHGGGCCC</SEQ_... |
Describe the effect of mutation Q07009-H262A on protein Calpain-2 catalytic subunit. | ### Wild-type:
MAGIAMKLAKDREAAEGLGSHERAIKYLNQDYETLRNECLEAGALFQDPSFPALPSSLGFKELGPYSSKTRGIEWKRPTEICADPQFIIGGATRTDICQGALGDCWLLAAIASLTLNEEILARVVPLDQSFQENYAGIFHFQFWQYGEWVEVVVDDRLPTKDGELLFVHSAEGSEFWSALLEKAYAKINGCYEALSGGATTEGFEDFTGGIAEWYELRKPPPNLFKIIQKALEKGSLLGCSIDITSAADSEAVTYQKLVKGHAYSVTGAEEVESSGSLQKLIRIRNPWGQVEWTGKWNDN
###... | Loss of activity. Mutant had no activity. The results suggest that H262 is part of the catalytic triad in calpain. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MDLSESLHDFILVFLGSGLILGSLGVVFFTNTIFSAFSLGLVLVCVSLFYILSNSHFVAASQLLIYVGAINVLIIFAVMFMNGSEYDQNFRVWTVGDGITLMVCTSIFISQINTILDTSWHGIIWTTRPNQILEQDLISTSQQIGIHLSTDFFLPFELISIILLVALIGAIFVARQ
### Sequence 2:
MASSNVTLSNDEVLRLVKDWNFTWSVVFLLITIVLQYGYPSRSMFVYVIKMFVLWLLWPASMALSIFCAVYPIDLASQIISGILAATSCAMWISYFVQSIRLFMRTGSWW... | Non-Homologous |
Provide a drug-likeness assessment for this compound. | SMILES: CCC(NC1=NCCO1)c1cccs1
Descriptors: MW=210.3, LogP=2.17, TPSA=33.62, HBD=1, HBA=4 | Descriptors: MW=210.3, LogP=2.17, TPSA=33.62, HBD=1, HBA=4, QED=0.83, Lipinski violations=0. Overall the molecule is broadly compatible with common oral drug-like descriptors, and a relatively high QED score suggests good drug-likeness. |
Describe the effect of mutation Q9NPD8-R60E on protein Ubiquitin-conjugating enzyme E2 T. | ### Wild-type:
MQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLEVIIPERYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPPKGAWRPSLNIATVLTSIQLLMSEPNPDDPLMADISSEFKYNKPAFLKNARQWTEKHARQKQKADEEEMLDNLPEAGDSRVHNSTQKRKASQLVGIEKKFHPDV
### Mutant:
MQRASRLKRELHMLATEPPPGITCWQDKDQMDDLRAQILGGANTPYEKGVFKLEVIIPEEYPFEPPQIRFLTPIYHPNIDSAGRICLDVLKLPP... | Loss of FANCL-binding and of FANCL-dependent monoubiquitination of FANCD2. The atomic structure of the FANCL RING-Ube2T complex reveals a specific and extensive network of additional electrostatic and hydrophobic interactions. These specific interactions are required for selection of Ube2T over other E2s by FANCL. |
Based on the marker genes, describe the enriched biological pathway. | CD3D, CTLA4, IKZF2, IL2RA, CD4 | The marker profile suggests functional enrichment consistent with the typical biology of regulatory T cell. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MAVPARHTSKAKKNKRRTHYKLTAPSVKFDETTGDYSRSHRVSLKGYYKGHKIAKANAAE
### Sequence 2:
MNPLISAASVIAAGLAVGLASIGPGVGQGTAAGQAVEGIARQPEAEGKIRGTLLLSLAFMEALTIYGLVVALALLFANPFV
### Answer: | Non-Homologous |
Classify the pair below as homologous or non-homologous. | ### Sequence 1:
MATFTDAEIDELFETSGTVIDNIITAQGKPAETVGRSAIPQGKTKVLSAAWEKHGSIQPPASQDNPDRQDRSDKQPSTPEQTTPHDSPPATSADQPPTQATDEAVDTQLRTGASNSLLLMLDKLSNKSSNAKKGAHGRAPKRGITNVRLNSRGVNPVAETVRKDRRTKSRPPLETRAQT
### Sequence 2:
MATFTDAEIDELFETSGTVIDSIITAQGKPVETVGRSAIPRGKTKALSSAWEKHGSVQSPASQDTPDRQDRSDKQLSTPEQVTPHDSPPATSTDQPPTQAADEAGDT... | Homologous |
What are the official names of this protein? | ### Protein Sequence:
SYM_PSEPW
### Answer: | Methionine--tRNA ligase, Methionyl-tRNA synthetase, MetRS. |
Based on the evidence, describe the ligand-target relationship. | Target: VEGFR2
Ligand SMILES: Cc1cc(/C=C/C#N)cc(C)c1Nc1ccnc(Nc2ccc(C#N)cc2)n1
Evidence: No specific activity evidence is provided; the question is a general relationship inference. | Without supporting bioactivity evidence, the relationship between this ligand and vascular endothelial growth factor receptor 2 (VEGFR2) is best described as an uncharacterized or putative association rather than a confirmed binding claim. |
What is the protein family that this protein belongs to? | ### Protein Sequence:
RL35_PSEU2
### Answer: | Belongs to the bacterial ribosomal protein bL35 family. |
What are the official names of this protein? | ### Protein Sequence:
TMCA_SALTY
### Answer: | tRNA(Met) cytidine acetyltransferase TmcA. |
Based on the markers below, determine the cell type. | ITGA2B, PPBP, GP1BA | This cell is most consistent with megakaryocyte, a megakaryocyte. Key markers such as ITGA2B, GP1BA, PPBP support this identity. |
Identify the cell type from the given marker gene expression profile. | <cell>
GAD2:low GAD1:medium SLC32A1:medium
</cell> | This cell is most consistent with inhibitory neuron, an inhibitory (GABAergic) neuron. Key markers such as GAD2, GAD1, SLC32A1 support this identity. |
What is the protein family that this protein belongs to? | ### Protein Sequence:
DNAK_YERPP
### Answer: | Belongs to the heat shock protein 70 family. |
What is the protein family that this protein belongs to? | ### Protein Sequence:
HIS6_MAGSA
### Answer: | Belongs to the HisA/HisF family. |
What is the function of this protein? | ### Protein Sequence:
RS7_NITSB
### Answer: | One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center, probably blocks exit of the E-site tRNA. |
Summarize the physicochemical properties of this molecule. | OC[C@H]1OC(O)[C@H](O)[C@@H](O)[C@H]1O | This molecule is small and polar, with hydrophilic character. It contains hydroxyl, ether. Its descriptor profile: MW=180.16, LogP=-3.22, TPSA=110.38, HBD=5, HBA=6, QED=0.29. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MVRETRVRVARVYEDIDPDDGQRVLVDRIWPHGIRKDDQRVGIWCKDVAPSKELREWYHHQPERFDEFASRYQEELHDSAALAELRKLTGRSVVTPVTATRHVARSHAAVLAQLLNGR
### Sequence 2:
IQCKRVYDPAEQSDGYRILVDRLWPRGIKKTDLALDEWDKEITPSTELRKAFHGEVVDYATFREQYLAELAQHEQEGKRLADIAK---KQPLTLLYSAKNTTQNHALVLADWL
### Answer: | Homologous |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MAKRDYYEVLGISKDASKDEIKKAYRKLSKKYHPDINKEEGADEKFKEISEAYEVLSDDNKRASYDQFGHDGPQGFGGQGFNGSDFGGFSGFGGGGFEDIFSSFFGGGRQRDPNAPQKGDDLQYTMTLTFEEAVFGTTKEISIRKDVTCETCHGDGAKPGTSKKTCSYCNGAGHVAVEQNTILGRVRTEQVCPKCNGSGQEFEEACPTCHGKGTENKTVKLEVKVPEGVDNEQQIRLAGEGSPGVNGGPAGDLYVVFRVKPSETFKRDGDDIYYKLNVSFPQAALGDEIKIPTLNNEVMLTIPA... | Non-Homologous |
What is the protein family that this protein belongs to? | ### Protein Sequence:
HEN2_ARATH
### Answer: | Belongs to the DExH box helicase family. SKI2 subfamily. |
Identify the cell type from the given marker genes. | CDH1, KRT8, EPCAM, KRT18 | This cell is most consistent with epithelial cell, an epithelial cell. Key markers such as KRT18, EPCAM, CDH1 support this identity. |
Identify the cell type from the given marker genes. | ITGA2B, GP1BA, PPBP | This cell is most consistent with megakaryocyte, a megakaryocyte. Key markers such as PPBP, ITGA2B, GP1BA support this identity. |
Describe key molecular descriptors for the given SMILES. | CC(C)CCn1cc(C2(c3cccc(-c4cncnc4)c3)N=C(N)N(C)C2=O)cn1 | This molecule is medium-sized and polar, with moderately lipophilic character. It contains aromatic ring, amide, amine. Its descriptor profile: MW=403.49, LogP=2.42, TPSA=102.29, HBD=1, HBA=6, QED=0.68. |
Determine whether these two protein sequences are homologous. | ### Sequence 1:
MLLRSVWYKLGSLLIILPLTGCGYVRLKRANFQTDFTINRIPTQGDVYHDNYDLTFSLNFATSSKDSYGTGWLIDWKGDENKPSNTDPFLIYLATNLHVVDALRNPQDYEPYNKDSNGQDYGNRDITHFFALGKYTDPGLLGVETKEQSAFISIQTSAIPKTAYTANDFVDYQYDSLTKQWNKKSDQKDQTQEQTVIGQSWSYKPAYADFAVIEVPLFLDNVRDKQVFDYFVKPAIETYKKLGDTAQLFTEQNLKELEKETYIMLGYPVVESNIYAHILGQGKELRVTQQVNNQPVKKNYVLQT... | Homologous |
Describe key molecular descriptors for the given SMILES. | O=C(O)C(=Cc1ccc(Br)cc1)C(=O)O | This molecule is medium-sized and moderately polar, with moderately lipophilic character. It contains aromatic ring, hydroxyl, halide. Its descriptor profile: MW=271.07, LogP=2.0, TPSA=74.6, HBD=2, HBA=2, QED=0.5. |
What is the protein family that this protein belongs to? | ### Protein Sequence:
PLSX_STAAN
### Answer: | Belongs to the PlsX family. |
Classify the pair below as homologous or non-homologous. | ### Sequence 1:
MAEKRNIFLVGPMGAGKSTIGRQLAQQLNMEFFDSDQEIERRTGADVGWVFDVEGEEGFRDREEKVINELTEKQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLARTQRDKKRPLLQVDEPPREVLEALAKERNPLYEEIADVTIRTDDQSAKVVANQIINMLESN
### Sequence 2:
MAEKRNIFLVGPMGAGKSTIGRQLAQQLNMEFFDSDQEIERRTGADVGWVFDVEGEEGFRDREEKVINELTEKQGIVLATGGGSVKSRETRNRLSARGVVVYLETTIEKQLAR... | Homologous |
What is the protein family that this protein belongs to? | ### Protein Sequence:
Y3426_BACC7
### Answer: | Belongs to the UPF0303 family. |
Classify the pair below as homologous or non-homologous. | ### Sequence 1:
MDVFGRGRAATADDYRRFLERNSRAAAKLAAATTPTHTASSRQQPEVSARPRHRSLSSRRNSVPHYDPHAGAGGDGQLALSERPSGTLGALAMAAQRRKSIGRPDTPVNAAMGSALRSSQRPRGDVRNPRGEGQTQRGGSRGEANHAQRRQSVTQSTAARQTQPHQGRPRPRRNTLRHM
### Sequence 2:
MESVLNNEKAIVVFSGGQDSTTCLFYAKKHFKEVELVTFNYGQRHDTEIEVAKQIAQDQGMKHHVLDMSLLSQLTPNALTQHDMEITNNEDGIPNTFVPARNLLFLS... | Non-Homologous |
Given the expression strengths of marker genes, what cell type is this? | <cell>
IAPP:medium MAFA:medium INS:medium NKX6-1:low
</cell> | This cell is most consistent with pancreatic beta cell, a pancreatic beta cell secreting insulin. Key markers such as NKX6-1, MAFA, INS support this identity. |
Describe the effect of mutation Q9XHH2-R196D on protein Dynein axonemal light chain 1. | ### Wild-type:
MAKATTIKDAIRIFEERKSVVATEAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKISSLSGMENLRILSLGRNLIKKIENLDAVADTLEELWISYNQIASLSGIEKLVNLRVLYMSNNKITNWGEIDKLAALDKLEDLLLAGNPLYNDYKENNATSEYRIEVVKRLPNLKKLDGMPVDVDEREQANVARGG
### Mutant:
MAKATTIKDAIRIFEERKSVVATEAEKVELHGMIPPIEKMDATLSTLKACKHLALSTNNIEKISSLSGMENLRILSLGRNLIKKIENLDAVAD... | Reduces swimming velocity. Expression of mutant form of LC1 yields dominant-negative effects on swimming velocity, as the flagella continually beat out of phase and stall near or at the power/recovery stroke switchpoint. |
Classify the pair below as homologous or non-homologous. | ### Sequence 1:
MRGIILLSFVLTSCLAADAVPAAADAAAVTTTTPAGAAAAAATTATTAKANTAATTNTAAAAAAAADTLTTKGTTTGTAKTTGVTTGTAKTTATTAVTSDTAVAANPATMNPSELSIYSLTVTMNQAQLQNFLATHSSGAATAGATGTSVASGASGASLEDSTTTTAAAAAGGNGAATIDDTTKGLTFVTSRTLKPSSSATSQGSAQASGSGSNASQANAAGVYSTNSVLVFVSICIGFIGGSLGI
### Sequence 2:
MRGIILLSFVLTSCLAADAVPAAADAAAVTTTTPAGAAAA... | Homologous |
Describe the effect of mutation A0A2Z5XAU0-Y68A on protein Diels-Alderase phm7. | ### Wild-type:
MSEPTSSSSLDITSNCIIETPLQPSDFLPKSANLFPKFPERISVDSWELWEFDTFDTNGSVAFGCSLYRDARGVEQGGFHAEVNALWPDGTHWGETLYFAVSEVVENSDGTTGGKWLSKDGGSITFHIASDYTAAALDFNVPGKVSGTMELRNHANVSPTSNLPASDAEAQLCPGVYYTFPMGPVATSVTATFSSVGANGESRELFISSGYGGMVRGWSARPWPTFMNDAYYVVAQVGPYMLQILRTLGSVFVQHKPFAVARLYLDGSLVSAANTVVGDELTAHADDVKGDAVRLTKVQP
###... | Significantly decreases enzyme activity. The mutation in Fsa2 results in [functional changes]. |
Assess the drug-likeness of the given molecule. | SMILES: Cc1cc(Cl)ccc1OC1CCN(C[C@H](O)CNC(=O)c2c[nH]c(=O)c3cc(S(C)(=O)=O)ccc23)CC1
Descriptors: MW=548.06, LogP=2.53, TPSA=128.8, HBD=3, HBA=7 | Descriptors: MW=548.06, LogP=2.53, TPSA=128.8, HBD=3, HBA=7, QED=0.4, Lipinski violations=1. Overall the molecule is broadly compatible with common oral drug-like descriptors, and a lower QED score suggests limited drug-likeness. |
Identify the compound name from the given SMILES. | N#CN | The SMILES represents an unnamed molecule with MW=42.04, LogP=-0.57, TPSA=49.81. PubChem lookup would be required to retrieve a canonical compound name or synonyms. |
Predict the Foldseek 3Di structural alphabet sequence for the amino-acid sequence below. | ### Sequence 1D:
EKFRERLKELVVPKHVMDVVDEELSKLGLLDNHSSEFNVTRNYLDWLTSIPWGKYSNENLDLARAQAVLEEDHYGMEDVKKRILEFIAVSQLRGSTQGKILCFYGPPGVGKTSIARSIARALNREYFRFSVGGMTDVAEIKGHRRTYVGAMPGKIIQCLKKTKTENPLILIDEVDKIPSSALLELLDPEQNANFLDHYLDVPVDLSKVLFICTANVTDTIPEPLRDRMEMINVSGYVAQEKLAIAERYLVPQARALCGLDESKAKLSSDVLTLLIKQYCRESGVRNLQKQVEKVLRKSAYKIV... | <SEQ_3Di>DVLVVLPVVADADDVLVVVLVVLVVVCVVPPPDDLVNVLSVVLSVLSSLFGHHAADQWDLDLVLLLVLVVVQDPDPPVVSVVVNVLSVVCVVVVQSQAFAAEEAAAPFAPPVVVLVSVCVSTVFAEDEDEFAAPVDCCQPQNAASVDPRGDRHDVSVVRSVRVHLAHEYEYEALLRYVVVSVVLCRDLVNQCFAAHRHHRHTHHNSNYHYYYYHHDCPSRDVVVVVRYDYDYDWFDDLVVLLVCCVPPLLVVLCVVQVHDPQAEDDDSVVLSLCVQWVDLARHCPSVSVLSNQQNNVSVVCCVVPPRVHDY... |
Based on the top expressed genes, infer the cell type. | <cell>
MYH11 ACTA2 TAGLN CNN1
</cell> | This cell is most consistent with smooth muscle cell, a smooth muscle cell. Key markers such as CNN1, MYH11, ACTA2 support this identity. |
Describe the effect of mutation O04482-S82C on protein Ubiquitin carboxyl-terminal hydrolase 2. | ### Wild-type:
MSWCTIESDPGVFTELIQQMQVKGVQVEELYSLDSDSLNNLRPVYGLIFLFKWQAGEKDERPTIQDQVSNLFFANQVINNASATQAILAILLNSPEVDIGPELSALKEFTKNFPSDLKGLAINNSDSIRAAHNSFARPEPFVPEEQKAATKDDDVYHFISYIPVDGVLYELDGLKEGPISLGPCPGDQTGIEWLQMVQPVIQERIERYSQSEIRFNLLAVIKNRKDIYTAELKELQRQREQLLQQANTCVDKSEAEAVNALIAEVGSGIEAASDKIVMEEEKFMKWRTENIRRKHNYIPF
###... | Gain of deubiquitination activity. |
What are the official names of this protein? | ### Protein Sequence:
RNH_ECOSM
### Answer: | Ribonuclease H, RNase H. |
Describe the effect of mutation Q02ML7-D265A on protein CRISPR-associated endonuclease Cas1. | ### Wild-type:
MDDISPSELKTILHSKRANLYYLQHCRVLVNGGRVEYVTDEGRHSHYWNIPIANTTSLLLGTGTSITQAAMRELARAGVLVGFCGGGGTPLFSANEVDVEVSWLTPQSEYRPTEYLQRWVGFWFDEEKRLVAARHFQRARLERIRHSWLEDRVLRDAGFAVDATALAVAVEDSARALEQAPNHEHLLTEEARLSKRLFKLAAQATRYGEFVRAKRGSGGDPANRFLDHGNYLAYGLAATATWVLGIPHGLAVLHGKTRRGGLVFDVADLIKDSLILPQAFLSAMRGDEEQDFRQACLDNL
###... | Considerable decrease in endonuclease activity. Mutation of the D265 residue to alanine () affects the function of the Cas1 protein. |
Are these two protein sequences structurally related like paraphrases? | ### Sequence 1:
MAVQQNKKSRSRRDMRRSHDALTTAAVSVDKTTGETHLRHHVTADGYYCGRKVINK
### Sequence 2:
MKAYKGMLLTCDAAVKQLILSLDERNRFIIMDLDETHLLISPDRIDWLRAELEVELEKNTYTLEP
### Answer: | Non-Homologous |
End of preview.
OmniGene-4 SFT corpus
Supervised fine-tuning data for the OmniGene-4 / OmniGene-4-MM family. See https://github.com/maris205/omnigene4 for the training scripts that consume these files.
Files
| File | Rows | Used by | Description |
|---|---|---|---|
bio_sft_v2_train.jsonl |
~179K | Bio-SFT v2 | Eight task families: protein homology (BioPAWS), DNA, structure (3Di/DSSP), cell biology, molecules, mutation, structure prediction, general bio QA |
distill_seed.jsonl |
~6K | seed-only | Initial distillation seed used to bootstrap the v2 corpus |
train/omnigene_sft_v1_train.jsonl |
~179K | SFT v3 base | Same as v2 with cleaner schema and Alpaca template |
train/omnigene_sft_v1_train_with_remote.jsonl |
~199K | SFT v3-v5 (final) | Above + 20K BioPAWS protein_pair_remote rows; this is the file used by Bio-SFT v3, v4, v5, and the OmniGene-4-MM Stage 2/3 LoRA training |
eval/omnigene_sft_v1_eval.jsonl |
~1.5K | held-out eval | Used by 40-eval_omnigene4mm.py, 60-eval_stage2.py, 92-eval_stage3v3.py, etc. |
master/omnigene_sft_v1_master.jsonl |
~285K | (intermediate) | Pre-split master corpus before train/eval split |
master/cell_sft_master.jsonl |
~37K | task subset | Cell-biology SFT subset |
master/mol_sft_master.jsonl |
~50K | task subset | Molecule SFT subset |
stats/data_mix_report.json |
— | metadata | Per-category counts and ratios |
Schema
Each line is a JSON object with at least instruction, input, output,
and category. Some rows additionally carry task_name and subtask for
fine-grained accounting.
Citation
@article{wang2026omnigene4,
author = {Wang, Liang},
title = {{OmniGene-4}: A Unified Bio-Language MoE Model with Router-Level
Interpretability and Modality-Invariant Transfer},
year = {2026},
journal = {bioRxiv},
doi = {10.64898/2026.05.12.724542}
}
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