PMC:7605337 / 26564-28312 JSON TXT

Annnotations TAB JSON ListView MergeView

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T161","span":{"begin":137,"end":146},"obj":"Disease"},{"id":"T162","span":{"begin":148,"end":152},"obj":"Disease"},{"id":"T163","span":{"begin":260,"end":269},"obj":"Disease"},{"id":"T164","span":{"begin":593,"end":602},"obj":"Disease"},{"id":"T165","span":{"begin":719,"end":728},"obj":"Disease"},{"id":"T166","span":{"begin":746,"end":750},"obj":"Disease"},{"id":"T167","span":{"begin":804,"end":813},"obj":"Disease"},{"id":"T168","span":{"begin":826,"end":830},"obj":"Disease"},{"id":"T169","span":{"begin":894,"end":903},"obj":"Disease"},{"id":"T170","span":{"begin":921,"end":925},"obj":"Disease"},{"id":"T171","span":{"begin":1205,"end":1214},"obj":"Disease"},{"id":"T172","span":{"begin":1366,"end":1375},"obj":"Disease"},{"id":"T173","span":{"begin":1491,"end":1500},"obj":"Disease"}],"attributes":[{"id":"A161","pred":"mondo_id","subj":"T161","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A162","pred":"mondo_id","subj":"T162","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A163","pred":"mondo_id","subj":"T163","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A164","pred":"mondo_id","subj":"T164","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A165","pred":"mondo_id","subj":"T165","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A166","pred":"mondo_id","subj":"T166","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A167","pred":"mondo_id","subj":"T167","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A168","pred":"mondo_id","subj":"T168","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A169","pred":"mondo_id","subj":"T169","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A170","pred":"mondo_id","subj":"T170","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A171","pred":"mondo_id","subj":"T171","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A172","pred":"mondo_id","subj":"T172","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A173","pred":"mondo_id","subj":"T173","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"The correlated motions of RBD atoms were also analyzed with the DCCM based on the Cα atoms of RBD from the last 400 ns of simulation for nCOV-2019, SARS-COV, and extended mutant systems and the last 200 ns for the other mutant systems (Figure 6). The DCCM for nCOV-2019 showed a correlation between residues 490–505 (containing α5, L4 and β5 regions) and residues 440–455 (containing α4, L1 and β5 regions) shown in the red rectangle in Figure 6. This correlation showed the coordination of these regions for binding ACE2 effectively. Another important correlation that appears in the DCCM of nCOV-2019 is between residues 473–481 with residues 482–491. These residues are in L3 and β6 regions and their correlation in nCOV-2019 is stronger than SARS-COV. This is due to the presence of the β6 strand in nCOV-2019, whereas in SARS-COV these residues all belong to L3. This indicates that L3 in nCOV-2019 has evolved from SARS-COV to adopt a new secondary structure, which causes strong correlation and makes the loop act as a recognition region for binding. The correlation in L3 is shown as a blue rectangle in Figure 6. Some of the mutations disrupted the patterns of correlation and anticorrelation in nCOV-2019-wt. Mutation N487A showed a stronger correlation in L3 and β6 strand than the wild-type RBD. In mutation E484A, correlation in L3 is stronger than the nCOV-2019-wt. DCCM for other mutants are shown in Figure S6. It is worth mentioning that mutation F486A disrupts the DCCM of nCOV-2019 by introducing strong correlations in the core region of RBD as well as the extended loop region. Residue F486 resides in L3 and plays a crucial role in stabilizing the recognition loop by making a π-stacking interaction with residue Y83A on ACE2."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T183","span":{"begin":277,"end":278},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T184","span":{"begin":368,"end":371},"obj":"http://purl.obolibrary.org/obo/CLO_0001375"},{"id":"T185","span":{"begin":649,"end":652},"obj":"http://purl.obolibrary.org/obo/CLO_0054064"},{"id":"T186","span":{"begin":904,"end":907},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T187","span":{"begin":939,"end":940},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T188","span":{"begin":1024,"end":1025},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T189","span":{"begin":1092,"end":1093},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T190","span":{"begin":1241,"end":1242},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T191","span":{"begin":1636,"end":1637},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T192","span":{"begin":1697,"end":1698},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The correlated motions of RBD atoms were also analyzed with the DCCM based on the Cα atoms of RBD from the last 400 ns of simulation for nCOV-2019, SARS-COV, and extended mutant systems and the last 200 ns for the other mutant systems (Figure 6). The DCCM for nCOV-2019 showed a correlation between residues 490–505 (containing α5, L4 and β5 regions) and residues 440–455 (containing α4, L1 and β5 regions) shown in the red rectangle in Figure 6. This correlation showed the coordination of these regions for binding ACE2 effectively. Another important correlation that appears in the DCCM of nCOV-2019 is between residues 473–481 with residues 482–491. These residues are in L3 and β6 regions and their correlation in nCOV-2019 is stronger than SARS-COV. This is due to the presence of the β6 strand in nCOV-2019, whereas in SARS-COV these residues all belong to L3. This indicates that L3 in nCOV-2019 has evolved from SARS-COV to adopt a new secondary structure, which causes strong correlation and makes the loop act as a recognition region for binding. The correlation in L3 is shown as a blue rectangle in Figure 6. Some of the mutations disrupted the patterns of correlation and anticorrelation in nCOV-2019-wt. Mutation N487A showed a stronger correlation in L3 and β6 strand than the wild-type RBD. In mutation E484A, correlation in L3 is stronger than the nCOV-2019-wt. DCCM for other mutants are shown in Figure S6. It is worth mentioning that mutation F486A disrupts the DCCM of nCOV-2019 by introducing strong correlations in the core region of RBD as well as the extended loop region. Residue F486 resides in L3 and plays a crucial role in stabilizing the recognition loop by making a π-stacking interaction with residue Y83A on ACE2."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T96","span":{"begin":30,"end":35},"obj":"Chemical"},{"id":"T97","span":{"begin":85,"end":90},"obj":"Chemical"}],"attributes":[{"id":"A96","pred":"chebi_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A97","pred":"chebi_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"}],"text":"The correlated motions of RBD atoms were also analyzed with the DCCM based on the Cα atoms of RBD from the last 400 ns of simulation for nCOV-2019, SARS-COV, and extended mutant systems and the last 200 ns for the other mutant systems (Figure 6). The DCCM for nCOV-2019 showed a correlation between residues 490–505 (containing α5, L4 and β5 regions) and residues 440–455 (containing α4, L1 and β5 regions) shown in the red rectangle in Figure 6. This correlation showed the coordination of these regions for binding ACE2 effectively. Another important correlation that appears in the DCCM of nCOV-2019 is between residues 473–481 with residues 482–491. These residues are in L3 and β6 regions and their correlation in nCOV-2019 is stronger than SARS-COV. This is due to the presence of the β6 strand in nCOV-2019, whereas in SARS-COV these residues all belong to L3. This indicates that L3 in nCOV-2019 has evolved from SARS-COV to adopt a new secondary structure, which causes strong correlation and makes the loop act as a recognition region for binding. The correlation in L3 is shown as a blue rectangle in Figure 6. Some of the mutations disrupted the patterns of correlation and anticorrelation in nCOV-2019-wt. Mutation N487A showed a stronger correlation in L3 and β6 strand than the wild-type RBD. In mutation E484A, correlation in L3 is stronger than the nCOV-2019-wt. DCCM for other mutants are shown in Figure S6. It is worth mentioning that mutation F486A disrupts the DCCM of nCOV-2019 by introducing strong correlations in the core region of RBD as well as the extended loop region. Residue F486 resides in L3 and plays a crucial role in stabilizing the recognition loop by making a π-stacking interaction with residue Y83A on ACE2."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T163","span":{"begin":0,"end":246},"obj":"Sentence"},{"id":"T164","span":{"begin":247,"end":446},"obj":"Sentence"},{"id":"T165","span":{"begin":447,"end":534},"obj":"Sentence"},{"id":"T166","span":{"begin":535,"end":653},"obj":"Sentence"},{"id":"T167","span":{"begin":654,"end":755},"obj":"Sentence"},{"id":"T168","span":{"begin":756,"end":867},"obj":"Sentence"},{"id":"T169","span":{"begin":868,"end":1057},"obj":"Sentence"},{"id":"T170","span":{"begin":1058,"end":1121},"obj":"Sentence"},{"id":"T171","span":{"begin":1122,"end":1218},"obj":"Sentence"},{"id":"T172","span":{"begin":1219,"end":1307},"obj":"Sentence"},{"id":"T173","span":{"begin":1308,"end":1379},"obj":"Sentence"},{"id":"T174","span":{"begin":1380,"end":1426},"obj":"Sentence"},{"id":"T175","span":{"begin":1427,"end":1598},"obj":"Sentence"},{"id":"T176","span":{"begin":1599,"end":1748},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The correlated motions of RBD atoms were also analyzed with the DCCM based on the Cα atoms of RBD from the last 400 ns of simulation for nCOV-2019, SARS-COV, and extended mutant systems and the last 200 ns for the other mutant systems (Figure 6). The DCCM for nCOV-2019 showed a correlation between residues 490–505 (containing α5, L4 and β5 regions) and residues 440–455 (containing α4, L1 and β5 regions) shown in the red rectangle in Figure 6. This correlation showed the coordination of these regions for binding ACE2 effectively. Another important correlation that appears in the DCCM of nCOV-2019 is between residues 473–481 with residues 482–491. These residues are in L3 and β6 regions and their correlation in nCOV-2019 is stronger than SARS-COV. This is due to the presence of the β6 strand in nCOV-2019, whereas in SARS-COV these residues all belong to L3. This indicates that L3 in nCOV-2019 has evolved from SARS-COV to adopt a new secondary structure, which causes strong correlation and makes the loop act as a recognition region for binding. The correlation in L3 is shown as a blue rectangle in Figure 6. Some of the mutations disrupted the patterns of correlation and anticorrelation in nCOV-2019-wt. Mutation N487A showed a stronger correlation in L3 and β6 strand than the wild-type RBD. In mutation E484A, correlation in L3 is stronger than the nCOV-2019-wt. DCCM for other mutants are shown in Figure S6. It is worth mentioning that mutation F486A disrupts the DCCM of nCOV-2019 by introducing strong correlations in the core region of RBD as well as the extended loop region. Residue F486 resides in L3 and plays a crucial role in stabilizing the recognition loop by making a π-stacking interaction with residue Y83A on ACE2."}

LitCovid-PubTator