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PMC:7755033 / 20980-22587 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
365 99-103 Gene denotes ACE2 Gene:59272
366 188-192 Gene denotes Bank Gene:55024
367 228-231 Gene denotes pdb Gene:5131
368 196-199 Gene denotes PDB Gene:5131
369 93-98 Species denotes human Tax:9606
370 114-122 Species denotes SARS-CoV Tax:694009
371 127-137 Species denotes SARS-CoV-2 Tax:2697049
372 397-405 Chemical denotes hydrogen MESH:D006859
373 480-485 Chemical denotes water MESH:D014867
398 656-685 Gene denotes Angiotensin converting enzyme Gene:1636
399 943-949 Gene denotes Nsp-10 Gene:43740578
400 1115-1119 Gene denotes ACE2 Gene:59272
401 1068-1073 Gene denotes spike Gene:43740568
402 1008-1013 Gene denotes spike Gene:43740568
403 757-762 Gene denotes spike Gene:43740568
404 711-716 Gene denotes spike Gene:43740568
405 1121-1124 Gene denotes PDB Gene:5131
406 1039-1042 Gene denotes PDB Gene:5131
407 982-985 Gene denotes PDB Gene:5131
408 928-931 Gene denotes PDB Gene:5131
409 877-880 Gene denotes PDB Gene:5131
410 818-821 Gene denotes PDB Gene:5131
411 777-780 Gene denotes PDB Gene:5131
412 731-734 Gene denotes PDB Gene:5131
413 608-611 Gene denotes PDB Gene:5131
414 702-710 Species denotes SARS-CoV Tax:694009
415 746-756 Species denotes SARS-CoV-2 Tax:2697049
416 792-802 Species denotes SARS-CoV-2 Tax:2697049
417 833-841 Species denotes SARS-CoV Tax:694009
418 916-926 Species denotes SARS-CoV-2 Tax:2697049
419 970-980 Species denotes SARS-CoV-2 Tax:2697049
420 997-1007 Species denotes SARS-CoV-2 Tax:2697049
421 1057-1067 Species denotes SARS-CoV-2 Tax:2697049
428 1481-1485 Gene denotes ACE2 Gene:59272
429 1450-1458 Species denotes SARS-CoV Tax:694009
430 1460-1470 Species denotes SARS-CoV-2 Tax:2697049
431 1475-1480 Species denotes human Tax:9606
432 1440-1446 Gene denotes PL-pro Gene:43740578
433 1431-1434 Chemical denotes 3CL

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T178 0-4 Sentence denotes 2.4.
T179 6-50 Sentence denotes Selection and preparation of protein targets
T180 51-233 Sentence denotes The available X-ray crystal structures of human ACE2 receptor, SARS-CoV and SARS-CoV-2 protein targets were downloaded from Protein Data Bank in PDB format (http://www.rcsb.org/pdb).
T181 234-335 Sentence denotes Before docking analyses, the protein structures were subjected to refinement and energy minimization.
T182 336-496 Sentence denotes The refinement involved the addition of missing atoms, polar hydrogen atoms and Kollman charges to the residues and removal of crystallographic water-molecules.
T183 497-603 Sentence denotes These structures were visualized in Accelrys Biovia Discovery Studio 2017 R2 (Biovia, San Diego, CA, USA).
T184 604-655 Sentence denotes The PDB IDs of the target proteins were as follows:
T185 656-694 Sentence denotes Angiotensin converting enzyme (PDB ID:
T186 695-738 Sentence denotes 1O8A), SARS-CoV spike glycoprotein (PDB ID:
T187 739-784 Sentence denotes 5WRG), SARS-CoV-2 spike glycoprotein (PDB ID:
T188 785-825 Sentence denotes 6VXX), SARS-CoV-2 main protease (PDB ID:
T189 826-935 Sentence denotes 6LU7), SARS-CoV main protease (3CL-pro) structure (PDB ID: IP9U), papain like protease of SARS-CoV-2 (PDB ID:
T190 936-989 Sentence denotes 6W9C), Nsp-10/Nsp-16 complex from SARS-CoV-2 (PDB ID:
T191 990-1046 Sentence denotes 6W75), SARS-CoV-2 spike receptor-binding domain (PDB ID:
T192 1047-1128 Sentence denotes 6M0J) and SARS-CoV-2 spike receptor-binding domain (RBD) bound with ACE2 (PDB ID:
T193 1129-1135 Sentence denotes 6M0J).
T194 1136-1323 Sentence denotes The identification of protein ligand-binding sites was carried out using online server Metapocket 2.0 (http://metapocket.eml.org) which combines prediction of sites from four methods viz.
T195 1324-1394 Sentence denotes LIGSITE csc, PASS, Q-SiteFinder and SURFNET to improve the prediction.
T196 1395-1607 Sentence denotes The active site residues of enzymes 3CL-pro, PL-pro of SARS-CoV, SARS-CoV-2 and human ACE2 were found from review of literature (Báez-Santos et al., 2015; Chen et al., 2020; Guy et al., 2005; Zhang et al., 2020).