PMC:7605337 / 18007-18568 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T48","span":{"begin":211,"end":219},"obj":"Body_part"}],"attributes":[{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma13478"}],"text":"The dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt. The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval. Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T111","span":{"begin":302,"end":306},"obj":"Disease"},{"id":"T112","span":{"begin":315,"end":324},"obj":"Disease"}],"attributes":[{"id":"A111","pred":"mondo_id","subj":"T111","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A112","pred":"mondo_id","subj":"T112","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"The dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt. The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval. Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T114","span":{"begin":232,"end":233},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T115","span":{"begin":406,"end":407},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T116","span":{"begin":412,"end":414},"obj":"http://purl.obolibrary.org/obo/CLO_0008491"}],"text":"The dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt. The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval. Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T69","span":{"begin":223,"end":228},"obj":"Chemical"},{"id":"T70","span":{"begin":430,"end":438},"obj":"Chemical"},{"id":"T71","span":{"begin":534,"end":539},"obj":"Chemical"},{"id":"T72","span":{"begin":544,"end":552},"obj":"Chemical"}],"attributes":[{"id":"A69","pred":"chebi_id","subj":"T69","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A70","pred":"chebi_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/CHEBI_18276"},{"id":"A71","pred":"chebi_id","subj":"T71","obj":"http://purl.obolibrary.org/obo/CHEBI_17891"},{"id":"A72","pred":"chebi_id","subj":"T72","obj":"http://purl.obolibrary.org/obo/CHEBI_15339"}],"text":"The dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt. The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval. Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°."}

{"project":"LitCovid-sentences","denotations":[{"id":"T91","span":{"begin":0,"end":251},"obj":"Sentence"},{"id":"T92","span":{"begin":252,"end":429},"obj":"Sentence"},{"id":"T93","span":{"begin":430,"end":561},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt. The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval. Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°."}

{"project":"LitCovid-PubTator","denotations":[{"id":"434","span":{"begin":302,"end":310},"obj":"Species"},{"id":"435","span":{"begin":315,"end":319},"obj":"Species"},{"id":"436","span":{"begin":139,"end":143},"obj":"Chemical"},{"id":"437","span":{"begin":430,"end":438},"obj":"Chemical"},{"id":"438","span":{"begin":211,"end":228},"obj":"Disease"},{"id":"439","span":{"begin":462,"end":465},"obj":"Disease"}],"attributes":[{"id":"A434","pred":"tao:has_database_id","subj":"434","obj":"Tax:694009"},{"id":"A435","pred":"tao:has_database_id","subj":"435","obj":"Tax:2697049"},{"id":"A437","pred":"tao:has_database_id","subj":"437","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 dynamic cross-correlation maps (DCCM) were obtained using the MD_TASK package to identify the correlated motions of RBD residues.46 In DCCM, the cross-correlation matrix Cij is obtained from displacement of backbone Cα atoms at a time interval Δt. The DCCM was constructed using the last 400 ns of SARS-COV and nCOV-2019 and the extended mutant systems and last 200 ns of all other mutant systems with a 100 ps time interval. Hydrogen bonds were analyzed in VMD where the distance cutoff was 3.2Å and the angle cutoff between the donor and acceptor was 30°."}