PMC:7605337 / 18653-19310 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7605337","sourcedb":"PMC","sourceid":"7605337","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7605337","text":"The molecular mechanics Poisson-Boltzmann surface area (MMPBSA) method was applied to calculate the binding energy between RBD and ACE2 in all complexes.47,48 For SARS-COV and nCOV-2019, 200 snapshots of the last 400 ns and for the mutant systems and 100 snapshots of the last 200 ns simulation were used for the calculation of binding free energies with an interval of 2 ns. Simulation for a few mutant systems (Y449A, T478I, Y489A, and S494P) was extended to 400 ns, and the binding energies were calculated for the last 400 ns to assess the convergence of free energies. The binding free energy of a ligand–receptor complex can be calculated as:1 2 3 4 5","divisions":[{"label":"label","span":{"begin":648,"end":649}},{"label":"label","span":{"begin":650,"end":651}},{"label":"label","span":{"begin":652,"end":653}},{"label":"label","span":{"begin":654,"end":655}}],"tracks":[{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T113","span":{"begin":163,"end":167},"obj":"Disease"},{"id":"T114","span":{"begin":176,"end":185},"obj":"Disease"}],"attributes":[{"id":"A113","pred":"mondo_id","subj":"T113","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A114","pred":"mondo_id","subj":"T114","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"subj":"T113","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T114","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T117","span":{"begin":391,"end":392},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T118","span":{"begin":601,"end":602},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T119","span":{"begin":610,"end":626},"obj":"http://purl.obolibrary.org/obo/GO_0043235"},{"id":"T120","span":{"begin":652,"end":655},"obj":"http://purl.obolibrary.org/obo/CLO_0001302"}],"attributes":[{"subj":"T117","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T118","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T119","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T120","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T73","span":{"begin":603,"end":609},"obj":"Chemical"}],"attributes":[{"id":"A73","pred":"chebi_id","subj":"T73","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T95","span":{"begin":0,"end":375},"obj":"Sentence"},{"id":"T96","span":{"begin":376,"end":573},"obj":"Sentence"},{"id":"T97","span":{"begin":574,"end":657},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T95","pred":"source","obj":"LitCovid-sentences"},{"subj":"T96","pred":"source","obj":"LitCovid-sentences"},{"subj":"T97","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"443","span":{"begin":131,"end":135},"obj":"Gene"},{"id":"444","span":{"begin":163,"end":171},"obj":"Species"},{"id":"445","span":{"begin":176,"end":180},"obj":"Species"}],"attributes":[{"id":"A443","pred":"tao:has_database_id","subj":"443","obj":"Gene:59272"},{"id":"A444","pred":"tao:has_database_id","subj":"444","obj":"Tax:694009"},{"id":"A445","pred":"tao:has_database_id","subj":"445","obj":"Tax:2697049"},{"subj":"443","pred":"source","obj":"LitCovid-PubTator"},{"subj":"444","pred":"source","obj":"LitCovid-PubTator"},{"subj":"445","pred":"source","obj":"LitCovid-PubTator"}],"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_"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-MONDO","color":"#ecaf93","default":true},{"id":"LitCovid-PD-CLO","color":"#9593ec"},{"id":"LitCovid-PD-CHEBI","color":"#abec93"},{"id":"LitCovid-sentences","color":"#ec93c5"},{"id":"LitCovid-PubTator","color":"#93dfec"}]}]}}