PMC:7544943 / 11777-13050 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T14","span":{"begin":31,"end":38},"obj":"Body_part"}],"attributes":[{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott \u0026 Olson, 2010). AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy. It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space. A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro. A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro. The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results. The docked poses were ranked as per their binding affinities at the end of the docking run. The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017). The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005). The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T37","span":{"begin":479,"end":487},"obj":"Disease"},{"id":"T38","span":{"begin":592,"end":600},"obj":"Disease"},{"id":"T39","span":{"begin":670,"end":678},"obj":"Disease"},{"id":"T40","span":{"begin":694,"end":702},"obj":"Disease"}],"attributes":[{"id":"A37","pred":"mondo_id","subj":"T37","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A38","pred":"mondo_id","subj":"T38","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A39","pred":"mondo_id","subj":"T39","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A40","pred":"mondo_id","subj":"T40","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott \u0026 Olson, 2010). AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy. It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space. A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro. A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro. The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results. The docked poses were ranked as per their binding affinities at the end of the docking run. The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017). The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005). The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T47","span":{"begin":201,"end":204},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T48","span":{"begin":242,"end":243},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T49","span":{"begin":272,"end":273},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T50","span":{"begin":378,"end":379},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T51","span":{"begin":395,"end":396},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T52","span":{"begin":402,"end":403},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T53","span":{"begin":409,"end":410},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T54","span":{"begin":496,"end":497},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T55","span":{"begin":518,"end":519},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T56","span":{"begin":522,"end":524},"obj":"http://purl.obolibrary.org/obo/CLO_0053799"},{"id":"T57","span":{"begin":525,"end":526},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T58","span":{"begin":532,"end":533},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T59","span":{"begin":939,"end":945},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T60","span":{"begin":1013,"end":1016},"obj":"http://purl.obolibrary.org/obo/CLO_0050167"},{"id":"T61","span":{"begin":1262,"end":1265},"obj":"http://purl.obolibrary.org/obo/CLO_0050167"}],"text":"The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott \u0026 Olson, 2010). AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy. It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space. A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro. A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro. The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results. The docked poses were ranked as per their binding affinities at the end of the docking run. The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017). The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005). The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"256","span":{"begin":681,"end":685},"obj":"Gene"},{"id":"257","span":{"begin":490,"end":494},"obj":"Gene"},{"id":"258","span":{"begin":479,"end":489},"obj":"Species"},{"id":"259","span":{"begin":592,"end":602},"obj":"Species"},{"id":"260","span":{"begin":670,"end":680},"obj":"Species"},{"id":"261","span":{"begin":694,"end":704},"obj":"Species"}],"attributes":[{"id":"A256","pred":"tao:has_database_id","subj":"256","obj":"Gene:8673700"},{"id":"A257","pred":"tao:has_database_id","subj":"257","obj":"Gene:8673700"},{"id":"A258","pred":"tao:has_database_id","subj":"258","obj":"Tax:2697049"},{"id":"A259","pred":"tao:has_database_id","subj":"259","obj":"Tax:2697049"},{"id":"A260","pred":"tao:has_database_id","subj":"260","obj":"Tax:2697049"},{"id":"A261","pred":"tao:has_database_id","subj":"261","obj":"Tax:2697049"}],"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 prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott \u0026 Olson, 2010). AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy. It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space. A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro. A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro. The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results. The docked poses were ranked as per their binding affinities at the end of the docking run. The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017). The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005). The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T115","span":{"begin":0,"end":137},"obj":"Sentence"},{"id":"T116","span":{"begin":138,"end":233},"obj":"Sentence"},{"id":"T117","span":{"begin":234,"end":377},"obj":"Sentence"},{"id":"T118","span":{"begin":378,"end":495},"obj":"Sentence"},{"id":"T119","span":{"begin":496,"end":612},"obj":"Sentence"},{"id":"T120","span":{"begin":613,"end":790},"obj":"Sentence"},{"id":"T121","span":{"begin":791,"end":882},"obj":"Sentence"},{"id":"T122","span":{"begin":883,"end":1024},"obj":"Sentence"},{"id":"T123","span":{"begin":1025,"end":1135},"obj":"Sentence"},{"id":"T124","span":{"begin":1136,"end":1273},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott \u0026 Olson, 2010). AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy. It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space. A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro. A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro. The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results. The docked poses were ranked as per their binding affinities at the end of the docking run. The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017). The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005). The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017)."}

{"project":"2_test","denotations":[{"id":"32938313-19499576-56197380","span":{"begin":131,"end":135},"obj":"19499576"}],"text":"The prepared structures of the protein and ligand were subjected to molecular docking analysis using AutoDock Vina (Trott \u0026 Olson, 2010). AutoDock Vina is the newest member of the AutoDock family that has improved speed and accuracy. It uses a hybrid scoring function and a quasi-Newtonian optimization algorithm to find the lowest energy confirmations within the search space. A grid box of 40 Å × 65 Å × 70 Å was built with the centre of the box at (11.98, 0.60, 4.79) for the SARS-CoV-2 Mpro. A grid box of size 30 Å × 45 Å × 30 Å with centre at (−36.51, 30.69, 5.48) was prepared for the SARS-CoV-2 RBD Spro. The exhaustiveness of search was set at 20 and 8 for the SARS-CoV-2 Mpro and the SARS-CoV-2 RBD Spro, respectively, to compensate for the larger box volume and reliable results. The docked poses were ranked as per their binding affinities at the end of the docking run. The ligand interactions of the best-docked poses at the active sites of the macromolecule were extracted using PyMol (Schrödinger LLC, 2017). The ligand interactions were analysed using the 2D interaction plot in the Discovery Studio Visualizer (2005). The Coulombic electrostatic potential surface was determined with the help of the APBS plugin available in PyMol (Schrödinger LLC, 2017)."}