PMC:7291971 / 88142-88950 JSONTXT

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T1732","span":{"begin":192,"end":200},"obj":"SP_10"},{"id":"T1733","span":{"begin":300,"end":304},"obj":"CHEBI:24870;CHEBI:24870"},{"id":"T1734","span":{"begin":327,"end":335},"obj":"SP_10"},{"id":"T1735","span":{"begin":336,"end":341},"obj":"PR:000000125"},{"id":"T92593","span":{"begin":327,"end":335},"obj":"SP_10"},{"id":"T15931","span":{"begin":336,"end":341},"obj":"PR:000000125"},{"id":"T4088","span":{"begin":192,"end":200},"obj":"SP_10"},{"id":"T99586","span":{"begin":300,"end":304},"obj":"CHEBI:24870;CHEBI:24870"},{"id":"T11834","span":{"begin":327,"end":335},"obj":"SP_10"},{"id":"T76206","span":{"begin":336,"end":341},"obj":"PR:000000125"}],"text":"All calculations were performed using Autodock vina (The Scripps Research Institute, La Jolla, CA) on a MSI computer with a 2.30 GHz Intel Core i5-8300H. The solved X-ray crystal structure of SARS-CoV nsp14 (PDB 5C8T) was used as a static receptor for docking. Both the co-crystalized ligand SAM and ions were removed from the SARS-CoV nsp14 protein using VMD 1.9.3 software. The ligand structures were drawn and minimized using MarvinSketch (ChemAxon). Targeted protein and ligand structures with polar hydrogens were converted to the required PDBQT format using MGL Tools (version 1.5.6). The docking was performed with a search box located at x = −11.155, y = −40.77, z = −3.688 coordinates, with a search box size of 25 × 25 × 25 Å3. After calculations, PDB files were analyzed using Pymol (version 2.3)."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T117","span":{"begin":342,"end":349},"obj":"Body_part"},{"id":"T118","span":{"begin":463,"end":470},"obj":"Body_part"},{"id":"T119","span":{"begin":734,"end":736},"obj":"Body_part"}],"attributes":[{"id":"A117","pred":"fma_id","subj":"T117","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A118","pred":"fma_id","subj":"T118","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A119","pred":"fma_id","subj":"T119","obj":"http://purl.org/sig/ont/fma/fma66599"}],"text":"All calculations were performed using Autodock vina (The Scripps Research Institute, La Jolla, CA) on a MSI computer with a 2.30 GHz Intel Core i5-8300H. The solved X-ray crystal structure of SARS-CoV nsp14 (PDB 5C8T) was used as a static receptor for docking. Both the co-crystalized ligand SAM and ions were removed from the SARS-CoV nsp14 protein using VMD 1.9.3 software. The ligand structures were drawn and minimized using MarvinSketch (ChemAxon). Targeted protein and ligand structures with polar hydrogens were converted to the required PDBQT format using MGL Tools (version 1.5.6). The docking was performed with a search box located at x = −11.155, y = −40.77, z = −3.688 coordinates, with a search box size of 25 × 25 × 25 Å3. After calculations, PDB files were analyzed using Pymol (version 2.3)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1647","span":{"begin":504,"end":513},"obj":"Chemical"}],"attributes":[{"id":"A1647","pred":"tao:has_database_id","subj":"1647","obj":"MESH:D006859"}],"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":"All calculations were performed using Autodock vina (The Scripps Research Institute, La Jolla, CA) on a MSI computer with a 2.30 GHz Intel Core i5-8300H. The solved X-ray crystal structure of SARS-CoV nsp14 (PDB 5C8T) was used as a static receptor for docking. Both the co-crystalized ligand SAM and ions were removed from the SARS-CoV nsp14 protein using VMD 1.9.3 software. The ligand structures were drawn and minimized using MarvinSketch (ChemAxon). Targeted protein and ligand structures with polar hydrogens were converted to the required PDBQT format using MGL Tools (version 1.5.6). The docking was performed with a search box located at x = −11.155, y = −40.77, z = −3.688 coordinates, with a search box size of 25 × 25 × 25 Å3. After calculations, PDB files were analyzed using Pymol (version 2.3)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T105","span":{"begin":192,"end":200},"obj":"Disease"},{"id":"T106","span":{"begin":327,"end":335},"obj":"Disease"}],"attributes":[{"id":"A105","pred":"mondo_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A106","pred":"mondo_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"All calculations were performed using Autodock vina (The Scripps Research Institute, La Jolla, CA) on a MSI computer with a 2.30 GHz Intel Core i5-8300H. The solved X-ray crystal structure of SARS-CoV nsp14 (PDB 5C8T) was used as a static receptor for docking. Both the co-crystalized ligand SAM and ions were removed from the SARS-CoV nsp14 protein using VMD 1.9.3 software. The ligand structures were drawn and minimized using MarvinSketch (ChemAxon). Targeted protein and ligand structures with polar hydrogens were converted to the required PDBQT format using MGL Tools (version 1.5.6). The docking was performed with a search box located at x = −11.155, y = −40.77, z = −3.688 coordinates, with a search box size of 25 × 25 × 25 Å3. After calculations, PDB files were analyzed using Pymol (version 2.3)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T456","span":{"begin":102,"end":103},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T457","span":{"begin":122,"end":123},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T458","span":{"begin":230,"end":231},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T459","span":{"begin":622,"end":623},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T460","span":{"begin":700,"end":701},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T461","span":{"begin":734,"end":736},"obj":"http://purl.obolibrary.org/obo/CLO_0001577"}],"text":"All calculations were performed using Autodock vina (The Scripps Research Institute, La Jolla, CA) on a MSI computer with a 2.30 GHz Intel Core i5-8300H. The solved X-ray crystal structure of SARS-CoV nsp14 (PDB 5C8T) was used as a static receptor for docking. Both the co-crystalized ligand SAM and ions were removed from the SARS-CoV nsp14 protein using VMD 1.9.3 software. The ligand structures were drawn and minimized using MarvinSketch (ChemAxon). Targeted protein and ligand structures with polar hydrogens were converted to the required PDBQT format using MGL Tools (version 1.5.6). The docking was performed with a search box located at x = −11.155, y = −40.77, z = −3.688 coordinates, with a search box size of 25 × 25 × 25 Å3. After calculations, PDB files were analyzed using Pymol (version 2.3)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T994","span":{"begin":85,"end":87},"obj":"Chemical"},{"id":"T995","span":{"begin":285,"end":291},"obj":"Chemical"},{"id":"T996","span":{"begin":292,"end":295},"obj":"Chemical"},{"id":"T998","span":{"begin":300,"end":304},"obj":"Chemical"},{"id":"T999","span":{"begin":342,"end":349},"obj":"Chemical"},{"id":"T1000","span":{"begin":380,"end":386},"obj":"Chemical"},{"id":"T1001","span":{"begin":463,"end":470},"obj":"Chemical"},{"id":"T1002","span":{"begin":475,"end":481},"obj":"Chemical"}],"attributes":[{"id":"A994","pred":"chebi_id","subj":"T994","obj":"http://purl.obolibrary.org/obo/CHEBI_33336"},{"id":"A995","pred":"chebi_id","subj":"T995","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A996","pred":"chebi_id","subj":"T996","obj":"http://purl.obolibrary.org/obo/CHEBI_15414"},{"id":"A997","pred":"chebi_id","subj":"T996","obj":"http://purl.obolibrary.org/obo/CHEBI_67040"},{"id":"A998","pred":"chebi_id","subj":"T998","obj":"http://purl.obolibrary.org/obo/CHEBI_24870"},{"id":"A999","pred":"chebi_id","subj":"T999","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A1000","pred":"chebi_id","subj":"T1000","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"},{"id":"A1001","pred":"chebi_id","subj":"T1001","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A1002","pred":"chebi_id","subj":"T1002","obj":"http://purl.obolibrary.org/obo/CHEBI_52214"}],"text":"All calculations were performed using Autodock vina (The Scripps Research Institute, La Jolla, CA) on a MSI computer with a 2.30 GHz Intel Core i5-8300H. The solved X-ray crystal structure of SARS-CoV nsp14 (PDB 5C8T) was used as a static receptor for docking. Both the co-crystalized ligand SAM and ions were removed from the SARS-CoV nsp14 protein using VMD 1.9.3 software. The ligand structures were drawn and minimized using MarvinSketch (ChemAxon). Targeted protein and ligand structures with polar hydrogens were converted to the required PDBQT format using MGL Tools (version 1.5.6). The docking was performed with a search box located at x = −11.155, y = −40.77, z = −3.688 coordinates, with a search box size of 25 × 25 × 25 Å3. After calculations, PDB files were analyzed using Pymol (version 2.3)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T582","span":{"begin":0,"end":153},"obj":"Sentence"},{"id":"T583","span":{"begin":154,"end":260},"obj":"Sentence"},{"id":"T584","span":{"begin":261,"end":375},"obj":"Sentence"},{"id":"T585","span":{"begin":376,"end":453},"obj":"Sentence"},{"id":"T586","span":{"begin":454,"end":590},"obj":"Sentence"},{"id":"T587","span":{"begin":591,"end":737},"obj":"Sentence"},{"id":"T588","span":{"begin":738,"end":808},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"All calculations were performed using Autodock vina (The Scripps Research Institute, La Jolla, CA) on a MSI computer with a 2.30 GHz Intel Core i5-8300H. The solved X-ray crystal structure of SARS-CoV nsp14 (PDB 5C8T) was used as a static receptor for docking. Both the co-crystalized ligand SAM and ions were removed from the SARS-CoV nsp14 protein using VMD 1.9.3 software. The ligand structures were drawn and minimized using MarvinSketch (ChemAxon). Targeted protein and ligand structures with polar hydrogens were converted to the required PDBQT format using MGL Tools (version 1.5.6). The docking was performed with a search box located at x = −11.155, y = −40.77, z = −3.688 coordinates, with a search box size of 25 × 25 × 25 Å3. After calculations, PDB files were analyzed using Pymol (version 2.3)."}