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  1. data/clustering/metrics/davies_bouldin_heatmap__BioSimCSE-BioLinkBERT.png +0 -3
  2. data/clustering/metrics/davies_bouldin_heatmap__BiomedNLP-BiomedBERT.png +0 -3
  3. data/clustering/metrics/davies_bouldin_heatmap__SapBERT-from.png +0 -3
  4. data/clustering/metrics/davies_bouldin_heatmap__biobert-large.png +0 -3
  5. data/clustering/metrics/davies_bouldin_heatmap__biobert-v1.1.png +0 -3
  6. data/clustering/metrics/davies_bouldin_heatmap__bioformer-8L.png +0 -3
  7. data/clustering/metrics/davies_bouldin_heatmap__biomed_roberta_base.png +0 -3
  8. data/clustering/metrics/davies_bouldin_heatmap__pubmedbert-base.png +0 -3
  9. data/clustering/metrics/davies_bouldin_heatmap__scibert_scivocab_uncased.png +0 -3
  10. data/clustering/metrics/n_clusters_heatmap__BioSimCSE-BioLinkBERT.png +0 -3
  11. data/clustering/metrics/n_clusters_heatmap__BiomedNLP-BiomedBERT.png +0 -3
  12. data/clustering/metrics/n_clusters_heatmap__SapBERT-from.png +0 -3
  13. data/clustering/metrics/n_clusters_heatmap__biobert-large.png +0 -3
  14. data/clustering/metrics/n_clusters_heatmap__biobert-v1.1.png +0 -3
  15. data/clustering/metrics/n_clusters_heatmap__bioformer-8L.png +0 -3
  16. data/clustering/metrics/n_clusters_heatmap__biomed_roberta_base.png +0 -3
  17. data/clustering/metrics/n_clusters_heatmap__pubmedbert-base.png +0 -3
  18. data/clustering/metrics/n_clusters_heatmap__scibert_scivocab_uncased.png +0 -3
  19. data/clustering/metrics/silhouette_heatmap__BioSimCSE-BioLinkBERT.png +0 -3
  20. data/clustering/metrics/silhouette_heatmap__BiomedNLP-BiomedBERT.png +0 -3
  21. data/clustering/metrics/silhouette_heatmap__SapBERT-from.png +0 -3
  22. data/clustering/metrics/silhouette_heatmap__biobert-large.png +0 -3
  23. data/clustering/metrics/silhouette_heatmap__biobert-v1.1.png +0 -3
  24. data/clustering/metrics/silhouette_heatmap__bioformer-8L.png +0 -3
  25. data/clustering/metrics/silhouette_heatmap__biomed_roberta_base.png +0 -3
  26. data/clustering/metrics/silhouette_heatmap__pubmedbert-base.png +0 -3
  27. data/clustering/metrics/silhouette_heatmap__scibert_scivocab_uncased.png +0 -3
  28. data/clustering/model=NeuML__pubmedbert-base-embeddings/min=10/t=0.5_desalting_process_cluster.html +0 -0
  29. data/clustering/model=NeuML__pubmedbert-base-embeddings/min=10/t=0.5_elution_buffer_cluster.html +0 -0
  30. data/clustering/model=NeuML__pubmedbert-base-embeddings/min=10/t=0.5_enzyme_name_cluster.html +0 -0
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assumed per asymmetric unit)","~100 kDa",0],["31059757",0,"molecular_weight","31 kDa","~100 kDa",0],["9933629",0,"molecular_weight","23 kDa (subunit)","~100 kDa",0],["37498378",0,"molecular_weight","14.919 kDa","~100 kDa",0],["16239227",0,"molecular_weight","19.5 kDa (subunit)","~100 kDa",0],["16239227",1,"molecular_weight","19.5 kDa (subunit)","~100 kDa",0],["26228622",1,"molecular_weight","43.0 kDa (in Escherichia coli); 27.4 kDa (in mycobacteria)","~100 kDa",0],["33412198",0,"molecular_weight","~43.1 kDa (413 residues including N-terminal tags)","~100 kDa",0],["23615910",0,"molecular_weight","70 kDa (homodimer)","~100 kDa",0],["23615910",1,"molecular_weight","70 kDa (homodimer)","~100 kDa",0],["12939264",0,"molecular_weight","12.487 kDa","~100 kDa",0],["26469317",0,"molecular_weight","34 kDa","~100 kDa",0],["11796724",0,"molecular_weight","14.5 kDa","~100 kDa",0],["11796724",1,"molecular_weight","14.5 kDa","~100 kDa",0],["16984394",0,"molecular_weight","~45 kDa per monomer","~100 kDa",0],["16984394",1,"molecular_weight","~45 kDa per monomer","~100 kDa",0],["26396194",0,"molecular_weight","22.8 kDa","~100 kDa",0],["26396194",1,"molecular_weight","22.8 kDa","~100 kDa",0],["26396194",2,"molecular_weight","25.4 kDa (dimer in asymmetric unit)","~100 kDa",0],["15276840",0,"molecular_weight","17.9 kDa","~100 kDa",0],["15276840",1,"molecular_weight","17.7 kDa","~100 kDa",0],["15479239",0,"molecular_weight","20 kDa","~100 kDa",0],["25430994",2,"molecular_weight","~21 kDa (monomeric RpsACTD by DLS)","~100 kDa",0],["25430994",3,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",4,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",5,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",6,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",7,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",8,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",9,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",10,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",11,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["25430994",13,"molecular_weight","~21 kDa (by analogy to RpsACTD DLS)","~100 kDa",0],["18289677",0,"molecular_weight","27 kDa","~100 kDa",0],["22825853",0,"molecular_weight","52 kDa","~100 kDa",0],["26876563",0,"molecular_weight","37155.4 Da (measured by MS); theoretical 37155 Da (including His6 tag and LE residues)","~100 kDa",0],["30306715",0,"molecular_weight","28,710 Da","~100 kDa",0],["30306715",2,"molecular_weight","13,236 Da","NOISE",-1],["30306715",3,"molecular_weight","15,322 Da","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["18974870",2,"molecular_weight","~70 kDa","~100 kDa",0],["29360453",0,"molecular_weight","70 kDa","~100 kDa",0],["20805881",0,"molecular_weight","57 kDa","~100 kDa",0],["33609202",0,"molecular_weight","28 kDa","~100 kDa",0],["26984196",2,"molecular_weight","~69 kDa","~100 kDa",0],["26984196",3,"molecular_weight","~69 kDa","~100 kDa",0],["25359607",0,"molecular_weight","38 kDa","~100 kDa",0],["10542234",0,"molecular_weight","45\u002f47 kDa","~100 kDa",0],["10542234",1,"molecular_weight","45\u002f47 kDa","~100 kDa",0],["10542234",2,"molecular_weight","45\u002f47 kDa","~100 kDa",0],["10542234",3,"molecular_weight","45\u002f47 kDa","~100 kDa",0],["22115998",0,"molecular_weight","33,590 Da (monomer); 71,170 Da (dimer)","~100 kDa",0],["24737322",0,"molecular_weight","18.34 kDa","~100 kDa",0],["8617763",0,"molecular_weight","33 kDa","~100 kDa",0],["15701515",0,"molecular_weight","~20 kDa (including His-tag)","~100 kDa",0],["15701515",1,"molecular_weight","~20 kDa (including His-tag)","~100 kDa",0],["20103719",0,"molecular_weight","20,743 Da (including His6-tag)","~100 kDa",0],["20103719",1,"molecular_weight","20,275 Da (including His6-tag)","~100 kDa",0],["16468985",0,"molecular_weight","∼730 kDa (measured); 750 kDa (predicted)","~100 kDa",0],["29174965",0,"molecular_weight","37 kDa","~100 kDa",0],["21283666",0,"molecular_weight","22.8 kDa (experimental); 19.6 kDa (theoretical)","~100 kDa",0],["22023140",0,"molecular_weight","17.5 kDa","~100 kDa",0],["18461140",0,"molecular_weight","27.5 kDa","~100 kDa",0],["18461140",1,"molecular_weight","93.0 kDa","~100 kDa",0],["18461140",2,"molecular_weight","61.0 kDa","~100 kDa",0],["18461140",3,"molecular_weight","89.0 kDa","~100 kDa",0],["18461140",4,"molecular_weight","31.0 kDa","~100 kDa",0],["20188740",0,"molecular_weight","29.9 kDa","~100 kDa",0],["20188740",1,"molecular_weight","34.1 kDa","~100 kDa",0],["28082125",0,"molecular_weight","23,874 Da (subunit)","~100 kDa",0],["37747938",1,"molecular_weight","~37 kDa (expected for variants; wild-type not explicitly stated)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["37747938",3,"molecular_weight","~37 kDa","~100 kDa",0],["18505459",0,"molecular_weight","68 kDa","~100 kDa",0],["12163508",0,"molecular_weight","13.238 kDa","~100 kDa",0],["12163508",1,"molecular_weight","12.827 kDa","~100 kDa",0],["12354223",0,"molecular_weight","approximately 120 kDa (SDS–PAGE band)","~100 kDa",0],["17319935",0,"molecular_weight","71 kDa","~100 kDa",0],["18164314",0,"molecular_weight","20.9 kDa per monomer; SDS–PAGE ~25 kDa","~100 kDa",0],["19270703",0,"molecular_weight","74,786 ± 142 Da (MALDI-TOF; expected 74,787 Da)","~100 kDa",0],["15373841",0,"molecular_weight","36,313 Da","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["18420147",0,"molecular_weight","36,903 Da (monomer)","~100 kDa",0],["28469974",0,"molecular_weight","~700 kDa (dodecameric complex)","~100 kDa",0],["20633027",2,"molecular_weight","~60 kDa","~100 kDa",0],["19636956",0,"molecular_weight","~15 kDa","~100 kDa",0],["16337227",0,"molecular_weight","~37 kDa (including His-tag)","~100 kDa",0],["16337227",1,"molecular_weight","~37 kDa (including His-tag)","~100 kDa",0],["23286234",0,"molecular_weight","40 kDa","~100 kDa",0],["11007651",0,"molecular_weight","28.8 kDa","~100 kDa",0],["27729224",0,"molecular_weight","36 kDa (dimer)","~100 kDa",0],["16950391",0,"molecular_weight","50 kDa","~100 kDa",0],["24424575",0,"molecular_weight","23.18 kDa","~100 kDa",0],["24424575",1,"molecular_weight","23.18 kDa","~100 kDa",0],["24424575",2,"molecular_weight","23.18 kDa","~100 kDa",0],["18509457",0,"molecular_weight","29.5 kDa (monomer)","~100 kDa",0],["21914799",0,"molecular_weight","75,290 Da (subunit)","~100 kDa",0],["28669536",0,"molecular_weight","~32 kDa","~100 kDa",0],["28669536",1,"molecular_weight","~32 kDa","~100 kDa",0],["28669536",2,"molecular_weight","~32 kDa","~100 kDa",0],["20837474",0,"molecular_weight","25 kDa","~100 kDa",0],["20837474",1,"molecular_weight","55 kDa","~100 kDa",0],["26362239",0,"molecular_weight","23.8 kDa","~100 kDa",0],["25644473",0,"molecular_weight","16227.0 Da (monomer, untagged; after removal of initiating Met and with extra Gly post-TEV)","~100 kDa",0],["15703182",1,"molecular_weight","∼140 kDa (apparent, dimer)","~100 kDa",0],["15703182",2,"molecular_weight","∼140 kDa (apparent, dimer)","~100 kDa",0],["24723382",2,"molecular_weight","9.3 kDa","~100 kDa",0],["30292819",0,"molecular_weight","29,077 Da","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["16468986",0,"molecular_weight","750 kDa","~100 kDa",0],["15158675",0,"molecular_weight","45 kDa","~100 kDa",0],["17482646",0,"molecular_weight","~45 kDa (dimer)","~100 kDa",0],["17482646",1,"molecular_weight","~45 kDa (dimer)","~100 kDa",0],["25379378",0,"molecular_weight","70 kDa","~100 kDa",0],["37385399",0,"molecular_weight","45 kDa","~100 kDa",0],["37385399",1,"molecular_weight","45 kDa","~100 kDa",0],["37385399",2,"molecular_weight","45 kDa","~100 kDa",0],["37385399",3,"molecular_weight","45 kDa","~100 kDa",0],["35314194",0,"molecular_weight","23 kDa and 38 kDa bands (SDS-PAGE)","~100 kDa",0],["17174327",0,"molecular_weight","~88 kDa (dimer)","~100 kDa",0],["12387860",0,"molecular_weight","18.0 kDa","~100 kDa",0],["12387860",1,"molecular_weight","20.6 kDa","~100 kDa",0],["12387860",2,"molecular_weight","16.5 kDa","~100 kDa",0],["19854148",0,"molecular_weight","40,848 Da (His6–MCR); 38,966 Da (His6-tag removed MCR)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["7822223",0,"molecular_weight","43 kDa","~100 kDa",0],["15695811",0,"molecular_weight","~24–28 kDa (SEC elution ~24 kDa; DLS 28 kDa)","~100 kDa",0],["15695811",1,"molecular_weight","~24–28 kDa","~100 kDa",0],["15155722",0,"molecular_weight","~50 kDa (apparent)","~100 kDa",0],["28625787",0,"molecular_weight","34.652 kDa","~100 kDa",0],["18086676",0,"molecular_weight","59,783 Da (monomer)","~100 kDa",0],["15286723",0,"molecular_weight","~45 kDa (His6-tagged fusion)","~100 kDa",0],["22017312",9,"molecular_weight","8637 Da (with N-terminal Met) and 8506 Da (without Met)","NOISE",-1],["21830810",0,"molecular_weight","~30 kDa","~100 kDa",0],["21830810",1,"molecular_weight","~30 kDa (assumed similar; not specifically reported)","~100 kDa",0],["21830810",2,"molecular_weight","~30 kDa (assumed similar; not specifically reported)","~100 kDa",0],["19556970",0,"molecular_weight","10,093 Da (observed); 10,091 Da (expected)","NOISE",-1],["19556970",1,"molecular_weight","51,827 Da (observed); 51,826 Da (expected)","NOISE",-1],["23519417",0,"molecular_weight","31,263.8 Da (experimental; theoretical 31,246.8 Da)","NOISE",-1],["37238602",0,"molecular_weight","46.4 kDa (His-tagged); 44.6 kDa after TEV cleavage","~100 kDa",0],["37238602",1,"molecular_weight","20 kDa (His-tagged); 17.7 kDa after thrombin cleavage","~100 kDa",0],["18822333",0,"molecular_weight","39.5 kDa","~100 kDa",0],["12072441",0,"molecular_weight","23,192 Da (observed ESI-MS); 23,168 Da (calculated, N-terminal Met removed)","~100 kDa",0],["21672513",0,"molecular_weight","45,378.2 Da","~100 kDa",0],["30065086",0,"molecular_weight","35,455 Da","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["8663379",0,"molecular_weight","300 kDa","~100 kDa",0],["8663379",1,"molecular_weight","300 kDa","~100 kDa",0],["17272297",0,"molecular_weight","41.318 kDa (MALDI-TOF; theoretical 41.308 kDa)","~100 kDa",0],["17272297",1,"molecular_weight","43.384 kDa (E. coli RF2)","~100 kDa",0],["12377127",0,"molecular_weight","27314 Da (measured); 27345 Da (calculated)","NOISE",-1],["27667690",1,"molecular_weight","~40 kDa","~100 kDa",0],["11741950",1,"molecular_weight","330 kDa","~100 kDa",0],["18798563",0,"molecular_weight","13.7 kDa (gel filtration); 19.4 kDa (calculated from sequence)","~100 kDa",0],["15893507",1,"molecular_weight","12.5 kDa (monomer; apparent ~26.8 kDa by gel filtration)","~100 kDa",0],["11606592",0,"molecular_weight","~18 kDa","~100 kDa",0],["11606592",1,"molecular_weight","~18 kDa","~100 kDa",0],["11606592",2,"molecular_weight","~18 kDa","~100 kDa",0],["11606592",3,"molecular_weight","~18 kDa","~100 kDa",0],["23512413",0,"molecular_weight","33,141.03 Da","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["10835275",0,"molecular_weight","50 kDa","~100 kDa",0],["15296735",0,"molecular_weight","Apparent MW by gel filtration: 78,000; 117,000; 309,000 Da (concentration-dependent; assigned as monomer\u002fdimer\u002ftetramer). With ATP\u002fUTP: 337,000–347,000 Da. By DLS: 270,000 Da (0.7 mg\u002fml) and 480,000 Da (7 mg\u002fml); with ATP\u002fUTP: 250,000 Da.","NOISE",-1],["15145952",0,"molecular_weight","~60 kDa","~100 kDa",0],["12963379",0,"molecular_weight","62.8 kDa (apparent, gel filtration; dimer)","~100 kDa",0],["11243796",0,"molecular_weight","96,253 Da (monomer)","~100 kDa",0],["11243796",1,"molecular_weight","96,253 Da (monomer, assumed same as wild-type)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["11243796",2,"molecular_weight","96,253 Da (monomer, assumed same as wild-type)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["11850422",0,"molecular_weight","43 kDa","~100 kDa",0],["17825835",0,"molecular_weight","28,283 Da (monomer); 52.8 kDa by DLS (dimer)","~100 kDa",0],["19544567",0,"molecular_weight","~90 kDa","~100 kDa",0],["27918543",0,"molecular_weight","75 kDa","~100 kDa",0],["27918543",3,"molecular_weight","75 kDa","~100 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38,966 Da (His6-tag removed MCR)","NOISE",-1],["7822223",0,"molecular_weight","43 kDa","~100 kDa",0],["15695811",0,"molecular_weight","~24–28 kDa (SEC elution ~24 kDa; DLS 28 kDa)","~100 kDa",0],["15695811",1,"molecular_weight","~24–28 kDa","~100 kDa",0],["15155722",0,"molecular_weight","~50 kDa (apparent)","~100 kDa",0],["28625787",0,"molecular_weight","34.652 kDa","~100 kDa",0],["18086676",0,"molecular_weight","59,783 Da (monomer)","~100 kDa",0],["15286723",0,"molecular_weight","~45 kDa (His6-tagged fusion)","~100 kDa",0],["22017312",9,"molecular_weight","8637 Da (with N-terminal Met) and 8506 Da (without Met)","NOISE",-1],["21830810",0,"molecular_weight","~30 kDa","~100 kDa",0],["21830810",1,"molecular_weight","~30 kDa (assumed similar; not specifically reported)","~100 kDa",0],["21830810",2,"molecular_weight","~30 kDa (assumed similar; not specifically reported)","~100 kDa",0],["19556970",0,"molecular_weight","10,093 Da (observed); 10,091 Da (expected)","27085.5 Da",49],["19556970",1,"molecular_weight","51,827 Da (observed); 51,826 Da (expected)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["23519417",0,"molecular_weight","31,263.8 Da (experimental; theoretical 31,246.8 Da)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["37238602",0,"molecular_weight","46.4 kDa (His-tagged); 44.6 kDa after TEV cleavage","NOISE",-1],["37238602",1,"molecular_weight","20 kDa (His-tagged); 17.7 kDa after thrombin cleavage","NOISE",-1],["18822333",0,"molecular_weight","39.5 kDa","~100 kDa",0],["12072441",0,"molecular_weight","23,192 Da (observed ESI-MS); 23,168 Da (calculated, N-terminal Met removed)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["21672513",0,"molecular_weight","45,378.2 Da","26,000 Da",16],["30065086",0,"molecular_weight","35,455 Da","27085.5 Da",49],["8663379",0,"molecular_weight","300 kDa","~100 kDa",0],["8663379",1,"molecular_weight","300 kDa","~100 kDa",0],["17272297",0,"molecular_weight","41.318 kDa (MALDI-TOF; theoretical 41.308 kDa)","26,000 Da",16],["17272297",1,"molecular_weight","43.384 kDa (E. coli RF2)","NOISE",-1],["12377127",0,"molecular_weight","27314 Da (measured); 27345 Da (calculated)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["27667690",1,"molecular_weight","~40 kDa","~100 kDa",0],["11741950",1,"molecular_weight","330 kDa","~100 kDa",0],["18798563",0,"molecular_weight","13.7 kDa (gel filtration); 19.4 kDa (calculated from sequence)","~100 kDa",0],["15893507",1,"molecular_weight","12.5 kDa (monomer; apparent ~26.8 kDa by gel filtration)","~100 kDa",0],["11606592",0,"molecular_weight","~18 kDa","~100 kDa",0],["11606592",1,"molecular_weight","~18 kDa","~100 kDa",0],["11606592",2,"molecular_weight","~18 kDa","~100 kDa",0],["11606592",3,"molecular_weight","~18 kDa","~100 kDa",0],["23512413",0,"molecular_weight","33,141.03 Da","27085.5 Da",49],["10835275",0,"molecular_weight","50 kDa","~100 kDa",0],["15296735",0,"molecular_weight","Apparent MW by gel filtration: 78,000; 117,000; 309,000 Da (concentration-dependent; assigned as monomer\u002fdimer\u002ftetramer). With ATP\u002fUTP: 337,000–347,000 Da. By DLS: 270,000 Da (0.7 mg\u002fml) and 480,000 Da (7 mg\u002fml); with ATP\u002fUTP: 250,000 Da.","NOISE",-1],["15145952",0,"molecular_weight","~60 kDa","~100 kDa",0],["12963379",0,"molecular_weight","62.8 kDa (apparent, gel filtration; dimer)","~100 kDa",0],["11243796",0,"molecular_weight","96,253 Da (monomer)","~100 kDa",0],["11243796",1,"molecular_weight","96,253 Da (monomer, assumed same as wild-type)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["11243796",2,"molecular_weight","96,253 Da (monomer, assumed same as wild-type)","66,915 ± 30 Da (MALDI-TOF); 67,008 Da (ESI-MS); predicted 67,018 Da",22],["11850422",0,"molecular_weight","43 kDa","~100 kDa",0],["17825835",0,"molecular_weight","28,283 Da (monomer); 52.8 kDa by DLS (dimer)","~100 kDa",0],["19544567",0,"molecular_weight","~90 kDa","~100 kDa",0],["27918543",0,"molecular_weight","75 kDa","~100 kDa",0],["27918543",3,"molecular_weight","75 kDa","~100 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