PMC:7755033 / 20980-22587 JSONTXT

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Selection and preparation of protein targets\nThe 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). Before docking analyses, the protein structures were subjected to refinement and energy minimization. The refinement involved the addition of missing atoms, polar hydrogen atoms and Kollman charges to the residues and removal of crystallographic water-molecules. These structures were visualized in Accelrys Biovia Discovery Studio 2017 R2 (Biovia, San Diego, CA, USA).\nThe PDB IDs of the target proteins were as follows: Angiotensin converting enzyme (PDB ID: 1O8A), SARS-CoV spike glycoprotein (PDB ID: 5WRG), SARS-CoV-2 spike glycoprotein (PDB ID: 6VXX), SARS-CoV-2 main protease (PDB ID: 6LU7), SARS-CoV main protease (3CL-pro) structure (PDB ID: IP9U), papain like protease of SARS-CoV-2 (PDB ID: 6W9C), Nsp-10/Nsp-16 complex from SARS-CoV-2 (PDB ID: 6W75), SARS-CoV-2 spike receptor-binding domain (PDB ID: 6M0J) and SARS-CoV-2 spike receptor-binding domain (RBD) bound with ACE2 (PDB ID: 6M0J).\nThe 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. LIGSITE csc, PASS, Q-SiteFinder and SURFNET to improve the prediction. 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)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T178","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T179","span":{"begin":6,"end":50},"obj":"Sentence"},{"id":"T180","span":{"begin":51,"end":233},"obj":"Sentence"},{"id":"T181","span":{"begin":234,"end":335},"obj":"Sentence"},{"id":"T182","span":{"begin":336,"end":496},"obj":"Sentence"},{"id":"T183","span":{"begin":497,"end":603},"obj":"Sentence"},{"id":"T184","span":{"begin":604,"end":655},"obj":"Sentence"},{"id":"T185","span":{"begin":656,"end":694},"obj":"Sentence"},{"id":"T186","span":{"begin":695,"end":738},"obj":"Sentence"},{"id":"T187","span":{"begin":739,"end":784},"obj":"Sentence"},{"id":"T188","span":{"begin":785,"end":825},"obj":"Sentence"},{"id":"T189","span":{"begin":826,"end":935},"obj":"Sentence"},{"id":"T190","span":{"begin":936,"end":989},"obj":"Sentence"},{"id":"T191","span":{"begin":990,"end":1046},"obj":"Sentence"},{"id":"T192","span":{"begin":1047,"end":1128},"obj":"Sentence"},{"id":"T193","span":{"begin":1129,"end":1135},"obj":"Sentence"},{"id":"T194","span":{"begin":1136,"end":1323},"obj":"Sentence"},{"id":"T195","span":{"begin":1324,"end":1394},"obj":"Sentence"},{"id":"T196","span":{"begin":1395,"end":1607},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.4. Selection and preparation of protein targets\nThe 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). Before docking analyses, the protein structures were subjected to refinement and energy minimization. The refinement involved the addition of missing atoms, polar hydrogen atoms and Kollman charges to the residues and removal of crystallographic water-molecules. These structures were visualized in Accelrys Biovia Discovery Studio 2017 R2 (Biovia, San Diego, CA, USA).\nThe PDB IDs of the target proteins were as follows: Angiotensin converting enzyme (PDB ID: 1O8A), SARS-CoV spike glycoprotein (PDB ID: 5WRG), SARS-CoV-2 spike glycoprotein (PDB ID: 6VXX), SARS-CoV-2 main protease (PDB ID: 6LU7), SARS-CoV main protease (3CL-pro) structure (PDB ID: IP9U), papain like protease of SARS-CoV-2 (PDB ID: 6W9C), Nsp-10/Nsp-16 complex from SARS-CoV-2 (PDB ID: 6W75), SARS-CoV-2 spike receptor-binding domain (PDB ID: 6M0J) and SARS-CoV-2 spike receptor-binding domain (RBD) bound with ACE2 (PDB ID: 6M0J).\nThe 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. LIGSITE csc, PASS, Q-SiteFinder and SURFNET to improve the prediction. 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)."}