PMC:7441777 / 27662-28835 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T45","span":{"begin":10,"end":16},"obj":"Body_part"},{"id":"T46","span":{"begin":62,"end":69},"obj":"Body_part"},{"id":"T47","span":{"begin":858,"end":865},"obj":"Body_part"},{"id":"T48","span":{"begin":950,"end":952},"obj":"Body_part"},{"id":"T49","span":{"begin":1015,"end":1019},"obj":"Body_part"},{"id":"T50","span":{"begin":1075,"end":1077},"obj":"Body_part"},{"id":"T51","span":{"begin":1155,"end":1162},"obj":"Body_part"}],"attributes":[{"id":"A45","pred":"fma_id","subj":"T45","obj":"http://purl.org/sig/ont/fma/fma23463"},{"id":"A46","pred":"fma_id","subj":"T46","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A47","pred":"fma_id","subj":"T47","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A48","pred":"fma_id","subj":"T48","obj":"http://purl.org/sig/ont/fma/fma66595"},{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma9712"},{"id":"A50","pred":"fma_id","subj":"T50","obj":"http://purl.org/sig/ont/fma/fma66595"},{"id":"A51","pred":"fma_id","subj":"T51","obj":"http://purl.org/sig/ont/fma/fma67257"}],"text":"Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T4","span":{"begin":1015,"end":1019},"obj":"Body_part"}],"attributes":[{"id":"A4","pred":"uberon_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/UBERON_0002398"}],"text":"Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T172","span":{"begin":228,"end":229},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T173","span":{"begin":237,"end":238},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T174","span":{"begin":246,"end":247},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T175","span":{"begin":255,"end":256},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T176","span":{"begin":264,"end":265},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T177","span":{"begin":273,"end":274},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T178","span":{"begin":282,"end":283},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T179","span":{"begin":291,"end":292},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T180","span":{"begin":303,"end":304},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T181","span":{"begin":405,"end":408},"obj":"http://purl.obolibrary.org/obo/CLO_0009325"},{"id":"T182","span":{"begin":883,"end":884},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T183","span":{"begin":950,"end":952},"obj":"http://purl.obolibrary.org/obo/CLO_0001562"},{"id":"T184","span":{"begin":950,"end":952},"obj":"http://purl.obolibrary.org/obo/CLO_0001563"},{"id":"T185","span":{"begin":1075,"end":1077},"obj":"http://purl.obolibrary.org/obo/CLO_0001562"},{"id":"T186","span":{"begin":1075,"end":1077},"obj":"http://purl.obolibrary.org/obo/CLO_0001563"}],"text":"Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T388","span":{"begin":62,"end":69},"obj":"Chemical"},{"id":"T389","span":{"begin":329,"end":339},"obj":"Chemical"},{"id":"T390","span":{"begin":341,"end":345},"obj":"Chemical"},{"id":"T391","span":{"begin":347,"end":350},"obj":"Chemical"},{"id":"T392","span":{"begin":364,"end":373},"obj":"Chemical"},{"id":"T394","span":{"begin":375,"end":388},"obj":"Chemical"},{"id":"T395","span":{"begin":390,"end":400},"obj":"Chemical"},{"id":"T396","span":{"begin":531,"end":538},"obj":"Chemical"},{"id":"T397","span":{"begin":634,"end":644},"obj":"Chemical"},{"id":"T398","span":{"begin":779,"end":788},"obj":"Chemical"},{"id":"T399","span":{"begin":858,"end":865},"obj":"Chemical"},{"id":"T400","span":{"begin":981,"end":990},"obj":"Chemical"},{"id":"T401","span":{"begin":1062,"end":1065},"obj":"Chemical"},{"id":"T402","span":{"begin":1126,"end":1129},"obj":"Chemical"},{"id":"T403","span":{"begin":1155,"end":1162},"obj":"Chemical"}],"attributes":[{"id":"A388","pred":"chebi_id","subj":"T388","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A389","pred":"chebi_id","subj":"T389","obj":"http://purl.obolibrary.org/obo/CHEBI_145994"},{"id":"A390","pred":"chebi_id","subj":"T390","obj":"http://purl.obolibrary.org/obo/CHEBI_4806"},{"id":"A391","pred":"chebi_id","subj":"T391","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A392","pred":"chebi_id","subj":"T392","obj":"http://purl.obolibrary.org/obo/CHEBI_18152"},{"id":"A393","pred":"chebi_id","subj":"T392","obj":"http://purl.obolibrary.org/obo/CHEBI_58395"},{"id":"A394","pred":"chebi_id","subj":"T394","obj":"http://purl.obolibrary.org/obo/CHEBI_8695"},{"id":"A395","pred":"chebi_id","subj":"T395","obj":"http://purl.obolibrary.org/obo/CHEBI_28775"},{"id":"A396","pred":"chebi_id","subj":"T396","obj":"http://purl.obolibrary.org/obo/CHEBI_46787"},{"id":"A397","pred":"chebi_id","subj":"T397","obj":"http://purl.obolibrary.org/obo/CHEBI_26195"},{"id":"A398","pred":"chebi_id","subj":"T398","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A399","pred":"chebi_id","subj":"T399","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A400","pred":"chebi_id","subj":"T400","obj":"http://purl.obolibrary.org/obo/CHEBI_35222"},{"id":"A401","pred":"chebi_id","subj":"T401","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A402","pred":"chebi_id","subj":"T402","obj":"http://purl.obolibrary.org/obo/CHEBI_136608"},{"id":"A403","pred":"chebi_id","subj":"T403","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"}],"text":"Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion."}

{"project":"LitCovid-PubTator","denotations":[{"id":"685","span":{"begin":309,"end":313},"obj":"Gene"},{"id":"686","span":{"begin":352,"end":356},"obj":"Gene"},{"id":"687","span":{"begin":629,"end":633},"obj":"Gene"},{"id":"688","span":{"begin":931,"end":935},"obj":"Gene"},{"id":"689","span":{"begin":936,"end":940},"obj":"Gene"},{"id":"690","span":{"begin":976,"end":980},"obj":"Gene"},{"id":"691","span":{"begin":329,"end":339},"obj":"Chemical"},{"id":"692","span":{"begin":341,"end":345},"obj":"Chemical"},{"id":"693","span":{"begin":364,"end":373},"obj":"Chemical"},{"id":"694","span":{"begin":375,"end":388},"obj":"Chemical"},{"id":"695","span":{"begin":390,"end":400},"obj":"Chemical"},{"id":"696","span":{"begin":634,"end":644},"obj":"Chemical"},{"id":"697","span":{"begin":814,"end":818},"obj":"Chemical"}],"attributes":[{"id":"A685","pred":"tao:has_database_id","subj":"685","obj":"Gene:43740578"},{"id":"A686","pred":"tao:has_database_id","subj":"686","obj":"Gene:2959"},{"id":"A687","pred":"tao:has_database_id","subj":"687","obj":"Gene:43740578"},{"id":"A688","pred":"tao:has_database_id","subj":"688","obj":"Gene:43740578"},{"id":"A689","pred":"tao:has_database_id","subj":"689","obj":"Gene:2959"},{"id":"A690","pred":"tao:has_database_id","subj":"690","obj":"Gene:43740578"},{"id":"A691","pred":"tao:has_database_id","subj":"691","obj":"MESH:C000606551"},{"id":"A692","pred":"tao:has_database_id","subj":"692","obj":"MESH:C045651"},{"id":"A693","pred":"tao:has_database_id","subj":"693","obj":"MESH:C040015"},{"id":"A694","pred":"tao:has_database_id","subj":"694","obj":"MESH:C079163"},{"id":"A695","pred":"tao:has_database_id","subj":"695","obj":"MESH:D006569"},{"id":"A696","pred":"tao:has_database_id","subj":"696","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":"Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion."}

{"project":"LitCovid-PD-GlycoEpitope","denotations":[{"id":"T13","span":{"begin":405,"end":408},"obj":"GlycoEpitope"}],"attributes":[{"id":"A13","pred":"glyco_epitope_db_id","subj":"T13","obj":"http://www.glycoepitope.jp/epitopes/AN0049"}],"text":"Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion."}

{"project":"LitCovid-sentences","denotations":[{"id":"T263","span":{"begin":0,"end":191},"obj":"Sentence"},{"id":"T264","span":{"begin":192,"end":432},"obj":"Sentence"},{"id":"T265","span":{"begin":433,"end":517},"obj":"Sentence"},{"id":"T266","span":{"begin":518,"end":712},"obj":"Sentence"},{"id":"T267","span":{"begin":713,"end":764},"obj":"Sentence"},{"id":"T268","span":{"begin":765,"end":876},"obj":"Sentence"},{"id":"T269","span":{"begin":877,"end":1001},"obj":"Sentence"},{"id":"T270","span":{"begin":1002,"end":1079},"obj":"Sentence"},{"id":"T271","span":{"begin":1080,"end":1173},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Since the radius of gyration (RoG) helps us to understand the protein structural compactness, RoG of each complex was monitored and represented in Figure S3A in the Supplementary Information. The average values of RoG are 29.96 Å, 29.52 Å, 29.60 Å, 29.86 Å, 29.75 Å, 29.88 Å, 29.84 Å, 29.74 Å and 29.86 Å for RdRp complexed with remdesivir, EGCG, TF3, TF2b, TF2a, myricetin, quercetagetin, hesperidin and TF1 respectively (Table 3). This suggests that the structural compactness remained unchanged during simulations. Finally, the solvent-accessible surface area (SASA) was also explored, and the time evolution of SASA for four RdRp-polyphenol complexes are shown in Figure S3B in the Supplementary Information. The average values of SASA are reported in Table 3. Binding of an inhibitor to the substrate changes SASA and sometimes could greatly affect the protein structure. Here, a relatively higher SASA value was obtained for RdRp/TF2b (35462.9 Å2) compared to the other RdRp/inhibitor complexes. On the other hand, the lowest SASA value was noted for RdRp/TF3 (34080.2 Å2). Thus, it can be suggested that the binding of TF3 could potentially reduce protein expansion."}