PMC:7441777 / 12545-13255 JSONTXT

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T47","span":{"begin":122,"end":130},"obj":"Disease"},{"id":"T48","span":{"begin":442,"end":450},"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"}],"text":"The 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."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T84","span":{"begin":241,"end":242},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T85","span":{"begin":372,"end":373},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T86","span":{"begin":387,"end":388},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T87","span":{"begin":394,"end":395},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T88","span":{"begin":401,"end":402},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T89","span":{"begin":417,"end":420},"obj":"http://purl.obolibrary.org/obo/CLO_0001053"},{"id":"T90","span":{"begin":432,"end":433},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The 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."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T208","span":{"begin":50,"end":61},"obj":"Chemical"},{"id":"T209","span":{"begin":63,"end":73},"obj":"Chemical"},{"id":"T210","span":{"begin":79,"end":82},"obj":"Chemical"},{"id":"T212","span":{"begin":187,"end":193},"obj":"Chemical"},{"id":"T213","span":{"begin":290,"end":294},"obj":"Chemical"},{"id":"T214","span":{"begin":316,"end":323},"obj":"Chemical"},{"id":"T215","span":{"begin":515,"end":521},"obj":"Chemical"},{"id":"T216","span":{"begin":664,"end":670},"obj":"Chemical"},{"id":"T217","span":{"begin":671,"end":679},"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"}],"text":"The 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."}

{"project":"LitCovid-PubTator","denotations":[{"id":"343","span":{"begin":114,"end":118},"obj":"Gene"},{"id":"344","span":{"begin":453,"end":457},"obj":"Gene"},{"id":"345","span":{"begin":122,"end":132},"obj":"Species"},{"id":"346","span":{"begin":442,"end":452},"obj":"Species"},{"id":"347","span":{"begin":50,"end":61},"obj":"Chemical"},{"id":"348","span":{"begin":63,"end":73},"obj":"Chemical"},{"id":"349","span":{"begin":79,"end":82},"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"}],"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 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."}

{"project":"LitCovid-sentences","denotations":[{"id":"T138","span":{"begin":0,"end":182},"obj":"Sentence"},{"id":"T139","span":{"begin":183,"end":371},"obj":"Sentence"},{"id":"T140","span":{"begin":372,"end":495},"obj":"Sentence"},{"id":"T141","span":{"begin":496,"end":585},"obj":"Sentence"},{"id":"T142","span":{"begin":586,"end":710},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The 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."}