LitCovid-sentences  

PMC:7755033 / 20980-22587 JSONTXT 2 Projects

Annnotations TAB TSV DIC JSON TextAE

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).