PMC:7605337 / 43355-44193 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T62","span":{"begin":366,"end":373},"obj":"Body_part"},{"id":"T63","span":{"begin":688,"end":695},"obj":"Body_part"}],"attributes":[{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma82749"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma82749"}],"text":"Using PCA, the aFEL for nCOV-2019 and SARS-COV demonstrated that the former occupies only one low energy state whereas the latter forms two distinct low energy basins separated by a metastable state with a barrier of about 6–7.5 kcal/mol. This confirms that the level of binding for the RBD domain is weaker in SARS-COV due to the presence of two basins. Similarly, alanine-substitution for a few residues caused the FEL to degenerate into separate multiple low energy regions (Figure S4). Dominant motions in the RBD are visualized in Figure S5 using the first eigenvector of the PCA. nCOV-2019 and SARS-COV did not show any strong motion in the extended loop region. Porcupine plots of alanine-mutants demonstrated that mutant N487A shows large motion in the L1 region and Y449A, G447A, and E484A showed large motions in L3 (Figure S5)."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T296","span":{"begin":24,"end":33},"obj":"Disease"},{"id":"T297","span":{"begin":38,"end":42},"obj":"Disease"},{"id":"T298","span":{"begin":311,"end":315},"obj":"Disease"},{"id":"T299","span":{"begin":586,"end":595},"obj":"Disease"},{"id":"T300","span":{"begin":600,"end":604},"obj":"Disease"}],"attributes":[{"id":"A296","pred":"mondo_id","subj":"T296","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A297","pred":"mondo_id","subj":"T297","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A298","pred":"mondo_id","subj":"T298","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A299","pred":"mondo_id","subj":"T299","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A300","pred":"mondo_id","subj":"T300","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Using PCA, the aFEL for nCOV-2019 and SARS-COV demonstrated that the former occupies only one low energy state whereas the latter forms two distinct low energy basins separated by a metastable state with a barrier of about 6–7.5 kcal/mol. This confirms that the level of binding for the RBD domain is weaker in SARS-COV due to the presence of two basins. Similarly, alanine-substitution for a few residues caused the FEL to degenerate into separate multiple low energy regions (Figure S4). Dominant motions in the RBD are visualized in Figure S5 using the first eigenvector of the PCA. nCOV-2019 and SARS-COV did not show any strong motion in the extended loop region. Porcupine plots of alanine-mutants demonstrated that mutant N487A shows large motion in the L1 region and Y449A, G447A, and E484A showed large motions in L3 (Figure S5)."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T271","span":{"begin":180,"end":181},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T272","span":{"begin":204,"end":205},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T273","span":{"begin":391,"end":392},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T274","span":{"begin":417,"end":420},"obj":"http://purl.obolibrary.org/obo/CLO_0003078"},{"id":"T275","span":{"begin":543,"end":545},"obj":"http://purl.obolibrary.org/obo/CLO_0008933"},{"id":"T276","span":{"begin":834,"end":836},"obj":"http://purl.obolibrary.org/obo/CLO_0008933"}],"text":"Using PCA, the aFEL for nCOV-2019 and SARS-COV demonstrated that the former occupies only one low energy state whereas the latter forms two distinct low energy basins separated by a metastable state with a barrier of about 6–7.5 kcal/mol. This confirms that the level of binding for the RBD domain is weaker in SARS-COV due to the presence of two basins. Similarly, alanine-substitution for a few residues caused the FEL to degenerate into separate multiple low energy regions (Figure S4). Dominant motions in the RBD are visualized in Figure S5 using the first eigenvector of the PCA. nCOV-2019 and SARS-COV did not show any strong motion in the extended loop region. Porcupine plots of alanine-mutants demonstrated that mutant N487A shows large motion in the L1 region and Y449A, G447A, and E484A showed large motions in L3 (Figure S5)."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T132","span":{"begin":6,"end":9},"obj":"Chemical"},{"id":"T134","span":{"begin":366,"end":373},"obj":"Chemical"},{"id":"T135","span":{"begin":485,"end":487},"obj":"Chemical"},{"id":"T136","span":{"begin":543,"end":545},"obj":"Chemical"},{"id":"T137","span":{"begin":581,"end":584},"obj":"Chemical"},{"id":"T139","span":{"begin":688,"end":695},"obj":"Chemical"},{"id":"T140","span":{"begin":834,"end":836},"obj":"Chemical"}],"attributes":[{"id":"A132","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_36751"},{"id":"A133","pred":"chebi_id","subj":"T132","obj":"http://purl.obolibrary.org/obo/CHEBI_62248"},{"id":"A134","pred":"chebi_id","subj":"T134","obj":"http://purl.obolibrary.org/obo/CHEBI_16449"},{"id":"A135","pred":"chebi_id","subj":"T135","obj":"http://purl.obolibrary.org/obo/CHEBI_29401"},{"id":"A136","pred":"chebi_id","subj":"T136","obj":"http://purl.obolibrary.org/obo/CHEBI_29386"},{"id":"A137","pred":"chebi_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/CHEBI_36751"},{"id":"A138","pred":"chebi_id","subj":"T137","obj":"http://purl.obolibrary.org/obo/CHEBI_62248"},{"id":"A139","pred":"chebi_id","subj":"T139","obj":"http://purl.obolibrary.org/obo/CHEBI_16449"},{"id":"A140","pred":"chebi_id","subj":"T140","obj":"http://purl.obolibrary.org/obo/CHEBI_29386"}],"text":"Using PCA, the aFEL for nCOV-2019 and SARS-COV demonstrated that the former occupies only one low energy state whereas the latter forms two distinct low energy basins separated by a metastable state with a barrier of about 6–7.5 kcal/mol. This confirms that the level of binding for the RBD domain is weaker in SARS-COV due to the presence of two basins. Similarly, alanine-substitution for a few residues caused the FEL to degenerate into separate multiple low energy regions (Figure S4). Dominant motions in the RBD are visualized in Figure S5 using the first eigenvector of the PCA. nCOV-2019 and SARS-COV did not show any strong motion in the extended loop region. Porcupine plots of alanine-mutants demonstrated that mutant N487A shows large motion in the L1 region and Y449A, G447A, and E484A showed large motions in L3 (Figure S5)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T296","span":{"begin":0,"end":238},"obj":"Sentence"},{"id":"T297","span":{"begin":239,"end":354},"obj":"Sentence"},{"id":"T298","span":{"begin":355,"end":489},"obj":"Sentence"},{"id":"T299","span":{"begin":490,"end":668},"obj":"Sentence"},{"id":"T300","span":{"begin":669,"end":838},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Using PCA, the aFEL for nCOV-2019 and SARS-COV demonstrated that the former occupies only one low energy state whereas the latter forms two distinct low energy basins separated by a metastable state with a barrier of about 6–7.5 kcal/mol. This confirms that the level of binding for the RBD domain is weaker in SARS-COV due to the presence of two basins. Similarly, alanine-substitution for a few residues caused the FEL to degenerate into separate multiple low energy regions (Figure S4). Dominant motions in the RBD are visualized in Figure S5 using the first eigenvector of the PCA. nCOV-2019 and SARS-COV did not show any strong motion in the extended loop region. Porcupine plots of alanine-mutants demonstrated that mutant N487A shows large motion in the L1 region and Y449A, G447A, and E484A showed large motions in L3 (Figure S5)."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1067","span":{"begin":24,"end":28},"obj":"Species"},{"id":"1068","span":{"begin":38,"end":46},"obj":"Species"},{"id":"1069","span":{"begin":311,"end":319},"obj":"Species"},{"id":"1070","span":{"begin":586,"end":590},"obj":"Species"},{"id":"1071","span":{"begin":600,"end":608},"obj":"Species"},{"id":"1072","span":{"begin":366,"end":373},"obj":"Chemical"},{"id":"1073","span":{"begin":688,"end":695},"obj":"Chemical"}],"attributes":[{"id":"A1067","pred":"tao:has_database_id","subj":"1067","obj":"Tax:2697049"},{"id":"A1068","pred":"tao:has_database_id","subj":"1068","obj":"Tax:694009"},{"id":"A1069","pred":"tao:has_database_id","subj":"1069","obj":"Tax:694009"},{"id":"A1070","pred":"tao:has_database_id","subj":"1070","obj":"Tax:2697049"},{"id":"A1071","pred":"tao:has_database_id","subj":"1071","obj":"Tax:694009"},{"id":"A1072","pred":"tao:has_database_id","subj":"1072","obj":"MESH:D000409"},{"id":"A1073","pred":"tao:has_database_id","subj":"1073","obj":"MESH:D000409"}],"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":"Using PCA, the aFEL for nCOV-2019 and SARS-COV demonstrated that the former occupies only one low energy state whereas the latter forms two distinct low energy basins separated by a metastable state with a barrier of about 6–7.5 kcal/mol. This confirms that the level of binding for the RBD domain is weaker in SARS-COV due to the presence of two basins. Similarly, alanine-substitution for a few residues caused the FEL to degenerate into separate multiple low energy regions (Figure S4). Dominant motions in the RBD are visualized in Figure S5 using the first eigenvector of the PCA. nCOV-2019 and SARS-COV did not show any strong motion in the extended loop region. Porcupine plots of alanine-mutants demonstrated that mutant N487A shows large motion in the L1 region and Y449A, G447A, and E484A showed large motions in L3 (Figure S5)."}