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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T38","span":{"begin":342,"end":350},"obj":"Body_part"},{"id":"T39","span":{"begin":1099,"end":1110},"obj":"Body_part"},{"id":"T40","span":{"begin":1130,"end":1136},"obj":"Body_part"}],"attributes":[{"id":"A38","pred":"fma_id","subj":"T38","obj":"http://purl.org/sig/ont/fma/fma13478"},{"id":"A39","pred":"fma_id","subj":"T39","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A40","pred":"fma_id","subj":"T40","obj":"http://purl.org/sig/ont/fma/fma23463"}],"text":"The 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes. Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A). It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium. The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3). The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation. We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information). Overall, this suggests the convergence of our simulations."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T70","span":{"begin":165,"end":173},"obj":"Disease"}],"attributes":[{"id":"A70","pred":"mondo_id","subj":"T70","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes. Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A). It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium. The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3). The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation. We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information). Overall, this suggests the convergence of our simulations."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T141","span":{"begin":93,"end":96},"obj":"http://purl.obolibrary.org/obo/CLO_0009325"},{"id":"T142","span":{"begin":463,"end":464},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T143","span":{"begin":495,"end":496},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T144","span":{"begin":685,"end":686},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T145","span":{"begin":693,"end":694},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T146","span":{"begin":701,"end":702},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T147","span":{"begin":709,"end":710},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T148","span":{"begin":717,"end":718},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T149","span":{"begin":725,"end":726},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T150","span":{"begin":733,"end":734},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T151","span":{"begin":741,"end":742},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T152","span":{"begin":752,"end":753},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T153","span":{"begin":880,"end":883},"obj":"http://purl.obolibrary.org/obo/CLO_0009325"},{"id":"T154","span":{"begin":1128,"end":1129},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T155","span":{"begin":1142,"end":1143},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes. Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A). It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium. The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3). The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation. We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information). Overall, this suggests the convergence of our simulations."}

LitCovid-PD-CHEBI

LitCovid-PubTator

LitCovid-PD-GlycoEpitope

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T9","span":{"begin":93,"end":96},"obj":"GlycoEpitope"},{"id":"T10","span":{"begin":880,"end":883},"obj":"GlycoEpitope"}],"attributes":[{"id":"A9","pred":"glyco_epitope_db_id","subj":"T9","obj":"http://www.glycoepitope.jp/epitopes/AN0049"},{"id":"A10","pred":"glyco_epitope_db_id","subj":"T10","obj":"http://www.glycoepitope.jp/epitopes/AN0049"}],"text":"The 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes. Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A). It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium. The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3). The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation. We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information). Overall, this suggests the convergence of our simulations."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T232","span":{"begin":0,"end":284},"obj":"Sentence"},{"id":"T233","span":{"begin":285,"end":466},"obj":"Sentence"},{"id":"T234","span":{"begin":467,"end":634},"obj":"Sentence"},{"id":"T235","span":{"begin":635,"end":918},"obj":"Sentence"},{"id":"T236","span":{"begin":919,"end":1020},"obj":"Sentence"},{"id":"T237","span":{"begin":1021,"end":1242},"obj":"Sentence"},{"id":"T238","span":{"begin":1243,"end":1301},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The 150 ns production simulations carried out for nine systems (complex of remdesivir, EGCG, TF1, TF2a, TF2b, TF3, hesperidin, myricetin, and quercetagetin with the SARS-CoV-2 RdRp) were stable on the basis of the potential energy and total energy (data not shown) of those complexes. Subsequently, the root-mean-square deviations (RMSDs) of backbone atoms relative to their respective initial positions were calculated for each complex and are shown in Figure 3(A). It is evident from Figure 3(A) that all the nine studied systems drifted from their initial positions during the first 50 ns, and after that, they reached equilibrium. The average RMSD values were estimated to be 2.30 Å, 2.45 Å, 1.87 Å, 2.28 Å, 1.68 Å, 2.47 Å, 1.90 Å, 2.03 Å and 1.88 Å for RdRp/remdesivir, RdRp/EGCG, RdRp/TF3, RdRp/TF2b, RdRp/TF2a, RdRp/myricetin, RdRp/quercetagetin, RdRp/hesperidin, and RdRp/TF1 complexes, respectively (Table 3). The least deviation was observed for RdRp/TF2a, while RdRp/myricetin displayed the highest deviation. We also investigated structural variations in the binding site, including all amino acids that fall within a radius of 5 Å from the inhibitor, and the same trend was observed (Figure S2A in the Supplementary Information). Overall, this suggests the convergence of our simulations."}