PMC:7441777 / 26416-27661 JSONTXT

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T167","span":{"begin":151,"end":152},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T168","span":{"begin":186,"end":187},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T169","span":{"begin":336,"end":337},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T170","span":{"begin":398,"end":399},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T171","span":{"begin":475,"end":481},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"}],"text":"To identify the regions which are flexible, the root-mean-square fluctuations (RMSFs) of Cα atoms of each residue are calculated and shown in Figure 3(B). From this analysis, we can get a better insight into what extent the binding of remdesivir and natural polyphenols affects the residual flexibility of RdRp (mainly Nsp12). Figure 3(B) indicates that RdRp/remdesivir and RdRp-polyphenols shared a similar RMSF pattern. Notable dynamic fluctuations were located in the non-active site domain, including both N-terminals and C-terminal. Regions around Asn150, Asp260, Arg305, Asn360, and Phe440 are found to be more flexible compared to the other area for all complexes. The binding pocket residues, such as Asp452, Lys545, Lys551, Tyr455, Arg553, Ala554, Arg555, Thr556, Asp618, Tyr619, pro620, Lys621, Cys622, Asp623 Arg624, Asn691, Asp760, Asp761, Phe793, Met794, Ser795, Lys798, Trp800, Glu811, Phe812, and Ser814 exhibited considerably low fluctuations for all the RdRp-inhibitor complexes. In the case of RdRp/TF3 and RdRp/TF2a, the binding site residues displayed lesser fluctuations compared to the other RdRp-polyphenol complexes. This suggests that TF3 and TF2a are likely to be bound to RdRp more strongly than the other polyphenols."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T378","span":{"begin":92,"end":97},"obj":"Chemical"},{"id":"T379","span":{"begin":235,"end":245},"obj":"Chemical"},{"id":"T380","span":{"begin":258,"end":269},"obj":"Chemical"},{"id":"T381","span":{"begin":359,"end":369},"obj":"Chemical"},{"id":"T382","span":{"begin":379,"end":390},"obj":"Chemical"},{"id":"T383","span":{"begin":976,"end":985},"obj":"Chemical"},{"id":"T384","span":{"begin":1017,"end":1020},"obj":"Chemical"},{"id":"T385","span":{"begin":1119,"end":1129},"obj":"Chemical"},{"id":"T386","span":{"begin":1160,"end":1163},"obj":"Chemical"},{"id":"T387","span":{"begin":1233,"end":1244},"obj":"Chemical"}],"attributes":[{"id":"A378","pred":"chebi_id","subj":"T378","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A379","pred":"chebi_id","subj":"T379","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A380","pred":"chebi_id","subj":"T380","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A381","pred":"chebi_id","subj":"T381","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A382","pred":"chebi_id","subj":"T382","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A383","pred":"chebi_id","subj":"T383","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A384","pred":"chebi_id","subj":"T384","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A385","pred":"chebi_id","subj":"T385","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A386","pred":"chebi_id","subj":"T386","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A387","pred":"chebi_id","subj":"T387","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"}],"text":"To identify the regions which are flexible, the root-mean-square fluctuations (RMSFs) of Cα atoms of each residue are calculated and shown in Figure 3(B). From this analysis, we can get a better insight into what extent the binding of remdesivir and natural polyphenols affects the residual flexibility of RdRp (mainly Nsp12). Figure 3(B) indicates that RdRp/remdesivir and RdRp-polyphenols shared a similar RMSF pattern. Notable dynamic fluctuations were located in the non-active site domain, including both N-terminals and C-terminal. Regions around Asn150, Asp260, Arg305, Asn360, and Phe440 are found to be more flexible compared to the other area for all complexes. The binding pocket residues, such as Asp452, Lys545, Lys551, Tyr455, Arg553, Ala554, Arg555, Thr556, Asp618, Tyr619, pro620, Lys621, Cys622, Asp623 Arg624, Asn691, Asp760, Asp761, Phe793, Met794, Ser795, Lys798, Trp800, Glu811, Phe812, and Ser814 exhibited considerably low fluctuations for all the RdRp-inhibitor complexes. In the case of RdRp/TF3 and RdRp/TF2a, the binding site residues displayed lesser fluctuations compared to the other RdRp-polyphenol complexes. This suggests that TF3 and TF2a are likely to be bound to RdRp more strongly than the other polyphenols."}

{"project":"LitCovid-PubTator","denotations":[{"id":"652","span":{"begin":306,"end":310},"obj":"Gene"},{"id":"653","span":{"begin":354,"end":358},"obj":"Gene"},{"id":"654","span":{"begin":374,"end":378},"obj":"Gene"},{"id":"655","span":{"begin":971,"end":975},"obj":"Gene"},{"id":"656","span":{"begin":1012,"end":1016},"obj":"Gene"},{"id":"657","span":{"begin":1025,"end":1029},"obj":"Gene"},{"id":"658","span":{"begin":1114,"end":1118},"obj":"Gene"},{"id":"659","span":{"begin":1199,"end":1203},"obj":"Gene"},{"id":"660","span":{"begin":510,"end":511},"obj":"Gene"},{"id":"661","span":{"begin":235,"end":245},"obj":"Chemical"},{"id":"662","span":{"begin":258,"end":269},"obj":"Chemical"},{"id":"663","span":{"begin":359,"end":369},"obj":"Chemical"},{"id":"664","span":{"begin":379,"end":390},"obj":"Chemical"},{"id":"665","span":{"begin":553,"end":559},"obj":"Chemical"},{"id":"666","span":{"begin":561,"end":567},"obj":"Chemical"},{"id":"667","span":{"begin":569,"end":575},"obj":"Chemical"},{"id":"668","span":{"begin":577,"end":583},"obj":"Chemical"},{"id":"669","span":{"begin":589,"end":595},"obj":"Chemical"},{"id":"670","span":{"begin":1119,"end":1129},"obj":"Chemical"},{"id":"671","span":{"begin":1233,"end":1244},"obj":"Chemical"}],"attributes":[{"id":"A652","pred":"tao:has_database_id","subj":"652","obj":"Gene:43740578"},{"id":"A653","pred":"tao:has_database_id","subj":"653","obj":"Gene:43740578"},{"id":"A654","pred":"tao:has_database_id","subj":"654","obj":"Gene:43740578"},{"id":"A655","pred":"tao:has_database_id","subj":"655","obj":"Gene:43740578"},{"id":"A656","pred":"tao:has_database_id","subj":"656","obj":"Gene:43740578"},{"id":"A657","pred":"tao:has_database_id","subj":"657","obj":"Gene:43740578"},{"id":"A658","pred":"tao:has_database_id","subj":"658","obj":"Gene:43740578"},{"id":"A659","pred":"tao:has_database_id","subj":"659","obj":"Gene:43740578"},{"id":"A660","pred":"tao:has_database_id","subj":"660","obj":"Gene:43740575"},{"id":"A661","pred":"tao:has_database_id","subj":"661","obj":"MESH:C000606551"},{"id":"A662","pred":"tao:has_database_id","subj":"662","obj":"MESH:D059808"},{"id":"A663","pred":"tao:has_database_id","subj":"663","obj":"MESH:C000606551"},{"id":"A664","pred":"tao:has_database_id","subj":"664","obj":"MESH:D059808"},{"id":"A670","pred":"tao:has_database_id","subj":"670","obj":"MESH:D059808"},{"id":"A671","pred":"tao:has_database_id","subj":"671","obj":"MESH:D059808"}],"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":"To identify the regions which are flexible, the root-mean-square fluctuations (RMSFs) of Cα atoms of each residue are calculated and shown in Figure 3(B). From this analysis, we can get a better insight into what extent the binding of remdesivir and natural polyphenols affects the residual flexibility of RdRp (mainly Nsp12). Figure 3(B) indicates that RdRp/remdesivir and RdRp-polyphenols shared a similar RMSF pattern. Notable dynamic fluctuations were located in the non-active site domain, including both N-terminals and C-terminal. Regions around Asn150, Asp260, Arg305, Asn360, and Phe440 are found to be more flexible compared to the other area for all complexes. The binding pocket residues, such as Asp452, Lys545, Lys551, Tyr455, Arg553, Ala554, Arg555, Thr556, Asp618, Tyr619, pro620, Lys621, Cys622, Asp623 Arg624, Asn691, Asp760, Asp761, Phe793, Met794, Ser795, Lys798, Trp800, Glu811, Phe812, and Ser814 exhibited considerably low fluctuations for all the RdRp-inhibitor complexes. In the case of RdRp/TF3 and RdRp/TF2a, the binding site residues displayed lesser fluctuations compared to the other RdRp-polyphenol complexes. This suggests that TF3 and TF2a are likely to be bound to RdRp more strongly than the other polyphenols."}

{"project":"LitCovid-sentences","denotations":[{"id":"T255","span":{"begin":0,"end":154},"obj":"Sentence"},{"id":"T256","span":{"begin":155,"end":326},"obj":"Sentence"},{"id":"T257","span":{"begin":327,"end":421},"obj":"Sentence"},{"id":"T258","span":{"begin":422,"end":537},"obj":"Sentence"},{"id":"T259","span":{"begin":538,"end":671},"obj":"Sentence"},{"id":"T260","span":{"begin":672,"end":996},"obj":"Sentence"},{"id":"T261","span":{"begin":997,"end":1140},"obj":"Sentence"},{"id":"T262","span":{"begin":1141,"end":1245},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To identify the regions which are flexible, the root-mean-square fluctuations (RMSFs) of Cα atoms of each residue are calculated and shown in Figure 3(B). From this analysis, we can get a better insight into what extent the binding of remdesivir and natural polyphenols affects the residual flexibility of RdRp (mainly Nsp12). Figure 3(B) indicates that RdRp/remdesivir and RdRp-polyphenols shared a similar RMSF pattern. Notable dynamic fluctuations were located in the non-active site domain, including both N-terminals and C-terminal. Regions around Asn150, Asp260, Arg305, Asn360, and Phe440 are found to be more flexible compared to the other area for all complexes. The binding pocket residues, such as Asp452, Lys545, Lys551, Tyr455, Arg553, Ala554, Arg555, Thr556, Asp618, Tyr619, pro620, Lys621, Cys622, Asp623 Arg624, Asn691, Asp760, Asp761, Phe793, Met794, Ser795, Lys798, Trp800, Glu811, Phe812, and Ser814 exhibited considerably low fluctuations for all the RdRp-inhibitor complexes. In the case of RdRp/TF3 and RdRp/TF2a, the binding site residues displayed lesser fluctuations compared to the other RdRp-polyphenol complexes. This suggests that TF3 and TF2a are likely to be bound to RdRp more strongly than the other polyphenols."}