PMC:7784829 / 6399-7113 JSONTXT

{"project":"LitCovid-sentences","denotations":[{"id":"T51","span":{"begin":0,"end":81},"obj":"Sentence"},{"id":"T52","span":{"begin":82,"end":191},"obj":"Sentence"},{"id":"T53","span":{"begin":192,"end":282},"obj":"Sentence"},{"id":"T54","span":{"begin":283,"end":647},"obj":"Sentence"},{"id":"T55","span":{"begin":648,"end":714},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The X-ray crystal structure of spike surface glycoprotein of SARS-CoV (PDB entry: 6CRV, resolution = 3.2 Å) and co-crystallized structure of SARS-CoV-2 RBD with human ACE2 Protein (PDB entry: 6M0J, resolution = 2.45 Å) was retrieved from Protein Data Bank (https:/www.rscb.org/pdb). The protein structure was prepared using the Discovery Studio Visualizer (version 3.1) and AutoDock Tools (ADT; version 1.5.4) through different steps viz. removal of water molecules and co-crystallized ligand, addition of missing hydrogen atoms, addition of Gasteiger-Marsili and Kollman charges, merging of non-polar hydrogens, and assignment of rotatable bonds. The file was then saved in pdbqt file format for further analysis."}

{"project":"LitCovid-PubTator","denotations":[{"id":"177","span":{"begin":167,"end":171},"obj":"Gene"},{"id":"178","span":{"begin":251,"end":255},"obj":"Gene"},{"id":"179","span":{"begin":61,"end":69},"obj":"Species"},{"id":"180","span":{"begin":141,"end":151},"obj":"Species"},{"id":"181","span":{"begin":161,"end":166},"obj":"Species"},{"id":"182","span":{"begin":450,"end":455},"obj":"Chemical"},{"id":"183","span":{"begin":514,"end":522},"obj":"Chemical"},{"id":"184","span":{"begin":602,"end":611},"obj":"Chemical"},{"id":"185","span":{"begin":542,"end":559},"obj":"Disease"}],"attributes":[{"id":"A177","pred":"tao:has_database_id","subj":"177","obj":"Gene:59272"},{"id":"A178","pred":"tao:has_database_id","subj":"178","obj":"Gene:55024"},{"id":"A179","pred":"tao:has_database_id","subj":"179","obj":"Tax:694009"},{"id":"A180","pred":"tao:has_database_id","subj":"180","obj":"Tax:2697049"},{"id":"A181","pred":"tao:has_database_id","subj":"181","obj":"Tax:9606"},{"id":"A182","pred":"tao:has_database_id","subj":"182","obj":"MESH:D014867"},{"id":"A183","pred":"tao:has_database_id","subj":"183","obj":"MESH:D006859"},{"id":"A184","pred":"tao:has_database_id","subj":"184","obj":"MESH:D006859"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"The X-ray crystal structure of spike surface glycoprotein of SARS-CoV (PDB entry: 6CRV, resolution = 3.2 Å) and co-crystallized structure of SARS-CoV-2 RBD with human ACE2 Protein (PDB entry: 6M0J, resolution = 2.45 Å) was retrieved from Protein Data Bank (https:/www.rscb.org/pdb). The protein structure was prepared using the Discovery Studio Visualizer (version 3.1) and AutoDock Tools (ADT; version 1.5.4) through different steps viz. removal of water molecules and co-crystallized ligand, addition of missing hydrogen atoms, addition of Gasteiger-Marsili and Kollman charges, merging of non-polar hydrogens, and assignment of rotatable bonds. The file was then saved in pdbqt file format for further analysis."}