PMC:7441777 / 12501-13255 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7441777","sourcedb":"PMC","sourceid":"7441777","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7441777","text":"2.1.3. Docking studies using AutoDock Vina\nThe energy-minimized structure of all the natural polyphenols, remdesivir, and GTP were docked with the receptor (RdRp of SARS-CoV-2) using AutoDock Vina 1.1.2 (Trott \u0026 Olson, 2010). The ligand files were further saved in PDBQT file format, a modified PDB format containing atomic charges, atom type definitions for ligands, and topological information (rotatable bonds). A grid box (30 Å × 30 Å × 30 Å) centered at (121, 120, 125) Å for the SARS-CoV-2 RdRp, was used in the docking experiments. After the receptor-ligand preparation, docking runs were started from the command prompt. The lowest binding energy and best-docked conformation were considered as the ligand molecule with maximum binding affinity.","divisions":[{"label":"label","span":{"begin":0,"end":6}},{"label":"title","span":{"begin":8,"end":43}}],"tracks":[{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T47","span":{"begin":166,"end":174},"obj":"Disease"},{"id":"T48","span":{"begin":486,"end":494},"obj":"Disease"}],"attributes":[{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"subj":"T47","pred":"source","obj":"LitCovid-PD-MONDO"},{"subj":"T48","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T84","span":{"begin":285,"end":286},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T85","span":{"begin":416,"end":417},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T86","span":{"begin":431,"end":432},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T87","span":{"begin":438,"end":439},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T88","span":{"begin":445,"end":446},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T89","span":{"begin":461,"end":464},"obj":"http://purl.obolibrary.org/obo/CLO_0001053"},{"id":"T90","span":{"begin":476,"end":477},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T84","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T85","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T86","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T87","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T88","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T89","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T90","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T208","span":{"begin":94,"end":105},"obj":"Chemical"},{"id":"T209","span":{"begin":107,"end":117},"obj":"Chemical"},{"id":"T210","span":{"begin":123,"end":126},"obj":"Chemical"},{"id":"T212","span":{"begin":231,"end":237},"obj":"Chemical"},{"id":"T213","span":{"begin":334,"end":338},"obj":"Chemical"},{"id":"T214","span":{"begin":360,"end":367},"obj":"Chemical"},{"id":"T215","span":{"begin":559,"end":565},"obj":"Chemical"},{"id":"T216","span":{"begin":708,"end":714},"obj":"Chemical"},{"id":"T217","span":{"begin":715,"end":723},"obj":"Chemical"}],"attributes":[{"id":"A208","pred":"chebi_id","subj":"T208","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A209","pred":"chebi_id","subj":"T209","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A210","pred":"chebi_id","subj":"T210","obj":"http://purl.obolibrary.org/obo/CHEBI_15996"},{"id":"A211","pred":"chebi_id","subj":"T210","obj":"http://purl.obolibrary.org/obo/CHEBI_37565"},{"id":"A212","pred":"chebi_id","subj":"T212","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A213","pred":"chebi_id","subj":"T213","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A214","pred":"chebi_id","subj":"T214","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A215","pred":"chebi_id","subj":"T215","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A216","pred":"chebi_id","subj":"T216","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A217","pred":"chebi_id","subj":"T217","obj":"http://purl.obolibrary.org/obo/CHEBI_25367"},{"subj":"T208","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T209","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T210","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T212","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T213","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T214","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T215","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T216","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T217","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PubTator","denotations":[{"id":"343","span":{"begin":158,"end":162},"obj":"Gene"},{"id":"344","span":{"begin":497,"end":501},"obj":"Gene"},{"id":"345","span":{"begin":166,"end":176},"obj":"Species"},{"id":"346","span":{"begin":486,"end":496},"obj":"Species"},{"id":"347","span":{"begin":94,"end":105},"obj":"Chemical"},{"id":"348","span":{"begin":107,"end":117},"obj":"Chemical"},{"id":"349","span":{"begin":123,"end":126},"obj":"Chemical"}],"attributes":[{"id":"A343","pred":"tao:has_database_id","subj":"343","obj":"Gene:43740578"},{"id":"A344","pred":"tao:has_database_id","subj":"344","obj":"Gene:43740578"},{"id":"A345","pred":"tao:has_database_id","subj":"345","obj":"Tax:2697049"},{"id":"A346","pred":"tao:has_database_id","subj":"346","obj":"Tax:2697049"},{"id":"A347","pred":"tao:has_database_id","subj":"347","obj":"MESH:D059808"},{"id":"A348","pred":"tao:has_database_id","subj":"348","obj":"MESH:C000606551"},{"id":"A349","pred":"tao:has_database_id","subj":"349","obj":"MESH:D006160"},{"subj":"343","pred":"source","obj":"LitCovid-PubTator"},{"subj":"344","pred":"source","obj":"LitCovid-PubTator"},{"subj":"345","pred":"source","obj":"LitCovid-PubTator"},{"subj":"346","pred":"source","obj":"LitCovid-PubTator"},{"subj":"347","pred":"source","obj":"LitCovid-PubTator"},{"subj":"348","pred":"source","obj":"LitCovid-PubTator"},{"subj":"349","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_"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T136","span":{"begin":0,"end":6},"obj":"Sentence"},{"id":"T137","span":{"begin":8,"end":43},"obj":"Sentence"},{"id":"T138","span":{"begin":44,"end":226},"obj":"Sentence"},{"id":"T139","span":{"begin":227,"end":415},"obj":"Sentence"},{"id":"T140","span":{"begin":416,"end":539},"obj":"Sentence"},{"id":"T141","span":{"begin":540,"end":629},"obj":"Sentence"},{"id":"T142","span":{"begin":630,"end":754},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T136","pred":"source","obj":"LitCovid-sentences"},{"subj":"T137","pred":"source","obj":"LitCovid-sentences"},{"subj":"T138","pred":"source","obj":"LitCovid-sentences"},{"subj":"T139","pred":"source","obj":"LitCovid-sentences"},{"subj":"T140","pred":"source","obj":"LitCovid-sentences"},{"subj":"T141","pred":"source","obj":"LitCovid-sentences"},{"subj":"T142","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PD-MONDO","color":"#93dbec","default":true},{"id":"LitCovid-PD-CLO","color":"#ece393"},{"id":"LitCovid-PD-CHEBI","color":"#c993ec"},{"id":"LitCovid-PubTator","color":"#93ecaf"},{"id":"LitCovid-sentences","color":"#ec9593"}]}]}}