PMC:7544934 / 9383-10833 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"244","span":{"begin":41,"end":45},"obj":"Gene"},{"id":"245","span":{"begin":322,"end":326},"obj":"Gene"},{"id":"246","span":{"begin":1437,"end":1441},"obj":"Gene"},{"id":"247","span":{"begin":26,"end":36},"obj":"Species"},{"id":"248","span":{"begin":139,"end":149},"obj":"Chemical"},{"id":"249","span":{"begin":273,"end":283},"obj":"Chemical"},{"id":"250","span":{"begin":318,"end":321},"obj":"Chemical"},{"id":"251","span":{"begin":509,"end":517},"obj":"Chemical"},{"id":"252","span":{"begin":1098,"end":1106},"obj":"Chemical"},{"id":"253","span":{"begin":1417,"end":1427},"obj":"Chemical"}],"attributes":[{"id":"A244","pred":"tao:has_database_id","subj":"244","obj":"Gene:59272"},{"id":"A245","pred":"tao:has_database_id","subj":"245","obj":"Gene:59272"},{"id":"A246","pred":"tao:has_database_id","subj":"246","obj":"Gene:59272"},{"id":"A247","pred":"tao:has_database_id","subj":"247","obj":"Tax:2697049"},{"id":"A248","pred":"tao:has_database_id","subj":"248","obj":"MESH:D009271"},{"id":"A249","pred":"tao:has_database_id","subj":"249","obj":"MESH:D009271"},{"id":"A251","pred":"tao:has_database_id","subj":"251","obj":"MESH:D006859"},{"id":"A252","pred":"tao:has_database_id","subj":"252","obj":"MESH:D006859"},{"id":"A253","pred":"tao:has_database_id","subj":"253","obj":"MESH:D009271"}],"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 experimentally solved SARS CoV-2 RBD-ACE2 complex (PDB ID: 6M0J solved at 2.45 Å) was obtained from PDB (Lan et al., 2020). The ligand naltrexone (PubChem CID: 5360515) was extracted from the PubChem database. An attempt was made to dock to explore the binding mode of naltrexone onto the binding interface of the RBD-ACE2 complex using AutoDock version 4.2 (Morris et al., 2009) and AUTODOCK tools 1.5.6. Before docking, the protein was prepared by the removal of small molecules and waters. Then, polar-hydrogen atoms were added to the structure followed by Gasteiger charges calculation. Ligand centered map was generated with a spacing of 0.375 Å and grid dimensions of 46 × 46 × 46 Å3 (x-y-z) covering the biding interfaces residues (which includes the receptor-binding motif viz., RBM) of the complex (coordinates of central grid point of maps:-34.512, 20.978, 4.521). Default settings were used for all other parameters while performing docking with the number of GA run to 100. From the resultant docked conformations, the top-ranked conformation with the least free energy of binding, hydrogen-bonding and interatomic-bonding pattern was selected for further optimization by employing long term MD simulation. PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.) and BIOVIA Discovery Studio Visualizer version4.5 were employed used to visualize the inter-molecular contacts between naltrexone with RBD-ACE2 complex."}

{"project":"LitCovid-sentences","denotations":[{"id":"T77","span":{"begin":0,"end":62},"obj":"Sentence"},{"id":"T78","span":{"begin":63,"end":127},"obj":"Sentence"},{"id":"T79","span":{"begin":128,"end":163},"obj":"Sentence"},{"id":"T80","span":{"begin":164,"end":213},"obj":"Sentence"},{"id":"T81","span":{"begin":214,"end":409},"obj":"Sentence"},{"id":"T82","span":{"begin":410,"end":496},"obj":"Sentence"},{"id":"T83","span":{"begin":497,"end":594},"obj":"Sentence"},{"id":"T84","span":{"begin":595,"end":878},"obj":"Sentence"},{"id":"T85","span":{"begin":879,"end":989},"obj":"Sentence"},{"id":"T86","span":{"begin":990,"end":1222},"obj":"Sentence"},{"id":"T87","span":{"begin":1223,"end":1450},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The experimentally solved SARS CoV-2 RBD-ACE2 complex (PDB ID: 6M0J solved at 2.45 Å) was obtained from PDB (Lan et al., 2020). The ligand naltrexone (PubChem CID: 5360515) was extracted from the PubChem database. An attempt was made to dock to explore the binding mode of naltrexone onto the binding interface of the RBD-ACE2 complex using AutoDock version 4.2 (Morris et al., 2009) and AUTODOCK tools 1.5.6. Before docking, the protein was prepared by the removal of small molecules and waters. Then, polar-hydrogen atoms were added to the structure followed by Gasteiger charges calculation. Ligand centered map was generated with a spacing of 0.375 Å and grid dimensions of 46 × 46 × 46 Å3 (x-y-z) covering the biding interfaces residues (which includes the receptor-binding motif viz., RBM) of the complex (coordinates of central grid point of maps:-34.512, 20.978, 4.521). Default settings were used for all other parameters while performing docking with the number of GA run to 100. From the resultant docked conformations, the top-ranked conformation with the least free energy of binding, hydrogen-bonding and interatomic-bonding pattern was selected for further optimization by employing long term MD simulation. PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.) and BIOVIA Discovery Studio Visualizer version4.5 were employed used to visualize the inter-molecular contacts between naltrexone with RBD-ACE2 complex."}

{"project":"2_test","denotations":[{"id":"32930058-19399780-56195691","span":{"begin":378,"end":382},"obj":"19399780"}],"text":"The experimentally solved SARS CoV-2 RBD-ACE2 complex (PDB ID: 6M0J solved at 2.45 Å) was obtained from PDB (Lan et al., 2020). The ligand naltrexone (PubChem CID: 5360515) was extracted from the PubChem database. An attempt was made to dock to explore the binding mode of naltrexone onto the binding interface of the RBD-ACE2 complex using AutoDock version 4.2 (Morris et al., 2009) and AUTODOCK tools 1.5.6. Before docking, the protein was prepared by the removal of small molecules and waters. Then, polar-hydrogen atoms were added to the structure followed by Gasteiger charges calculation. Ligand centered map was generated with a spacing of 0.375 Å and grid dimensions of 46 × 46 × 46 Å3 (x-y-z) covering the biding interfaces residues (which includes the receptor-binding motif viz., RBM) of the complex (coordinates of central grid point of maps:-34.512, 20.978, 4.521). Default settings were used for all other parameters while performing docking with the number of GA run to 100. From the resultant docked conformations, the top-ranked conformation with the least free energy of binding, hydrogen-bonding and interatomic-bonding pattern was selected for further optimization by employing long term MD simulation. PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.) and BIOVIA Discovery Studio Visualizer version4.5 were employed used to visualize the inter-molecular contacts between naltrexone with RBD-ACE2 complex."}