PMC:7605337 / 16471-17542 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 last 400 ns of simulation was used to explore the dominant motions in SARS-COV, nCOV-2019 and the mutations with extended simulation, and last 200 ns for all other mutants using principal component analysis (PCA) as part of the quasiharmonic analysis method.44 For this method the rotational and translational motions of RBD of all systems were eliminated by fitting to a reference (crystal) structure. Next, 4000 snapshots from the last 400 ns of SARS-COV, nCOV-2019 and mutations with extended simulation time, and 2000 snapshots from last 200 ns of all other mutant systems were taken to generate the covariance matrix between Cα atoms of RBD. In the mutant systems with production run, the last 400 ns was used for this analysis. Diagonalization of this matrix resulted in a diagonal matrix of eigenvalues and their corresponding eigenvectors.43,45 The first eigenvector which indicate the first principal component was used to visualize the dominant global motions of all complexes through porcupine plots using the (PorcupinePlot.tcl) script in visual MD (VMD).","tracks":[{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T107","span":{"begin":74,"end":78},"obj":"Disease"},{"id":"T108","span":{"begin":84,"end":93},"obj":"Disease"},{"id":"T109","span":{"begin":452,"end":456},"obj":"Disease"},{"id":"T110","span":{"begin":462,"end":471},"obj":"Disease"}],"attributes":[{"id":"A107","pred":"mondo_id","subj":"T107","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A108","pred":"mondo_id","subj":"T108","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A109","pred":"mondo_id","subj":"T109","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A110","pred":"mondo_id","subj":"T110","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"subj":"T107","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T108","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T109","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T110","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T110","span":{"begin":374,"end":375},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T111","span":{"begin":781,"end":782},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T112","span":{"begin":1062,"end":1064},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"}],"attributes":[{"subj":"T110","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T111","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T112","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T65","span":{"begin":212,"end":215},"obj":"Chemical"},{"id":"T67","span":{"begin":637,"end":642},"obj":"Chemical"},{"id":"T68","span":{"begin":1062,"end":1064},"obj":"Chemical"}],"attributes":[{"id":"A65","pred":"chebi_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/CHEBI_36751"},{"id":"A66","pred":"chebi_id","subj":"T65","obj":"http://purl.obolibrary.org/obo/CHEBI_62248"},{"id":"A67","pred":"chebi_id","subj":"T67","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A68","pred":"chebi_id","subj":"T68","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"subj":"T65","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T67","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T68","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":300,"end":313},"obj":"http://purl.obolibrary.org/obo/GO_0006412"}],"attributes":[{"subj":"T5","pred":"source","obj":"LitCovid-PD-GO-BP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T85","span":{"begin":0,"end":406},"obj":"Sentence"},{"id":"T86","span":{"begin":407,"end":650},"obj":"Sentence"},{"id":"T87","span":{"begin":651,"end":737},"obj":"Sentence"},{"id":"T88","span":{"begin":738,"end":1071},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T85","pred":"source","obj":"LitCovid-sentences"},{"subj":"T86","pred":"source","obj":"LitCovid-sentences"},{"subj":"T87","pred":"source","obj":"LitCovid-sentences"},{"subj":"T88","pred":"source","obj":"LitCovid-sentences"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"420","span":{"begin":74,"end":82},"obj":"Species"},{"id":"421","span":{"begin":84,"end":88},"obj":"Species"},{"id":"422","span":{"begin":452,"end":460},"obj":"Species"},{"id":"423","span":{"begin":462,"end":466},"obj":"Species"},{"id":"424","span":{"begin":1055,"end":1064},"obj":"Disease"},{"id":"425","span":{"begin":1066,"end":1069},"obj":"Disease"}],"attributes":[{"id":"A420","pred":"tao:has_database_id","subj":"420","obj":"Tax:694009"},{"id":"A421","pred":"tao:has_database_id","subj":"421","obj":"Tax:2697049"},{"id":"A422","pred":"tao:has_database_id","subj":"422","obj":"Tax:694009"},{"id":"A423","pred":"tao:has_database_id","subj":"423","obj":"Tax:2697049"},{"id":"A424","pred":"tao:has_database_id","subj":"424","obj":"MESH:D009436"},{"subj":"420","pred":"source","obj":"LitCovid-PubTator"},{"subj":"421","pred":"source","obj":"LitCovid-PubTator"},{"subj":"422","pred":"source","obj":"LitCovid-PubTator"},{"subj":"423","pred":"source","obj":"LitCovid-PubTator"},{"subj":"424","pred":"source","obj":"LitCovid-PubTator"},{"subj":"425","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":"#b9ec93","default":true},{"id":"LitCovid-PD-CLO","color":"#ec93d3"},{"id":"LitCovid-PD-CHEBI","color":"#93eceb"},{"id":"LitCovid-PD-GO-BP","color":"#ecd193"},{"id":"LitCovid-sentences","color":"#b793ec"},{"id":"LitCovid-PubTator","color":"#93ec9d"}]}]}}