PMC:7605337 / 28572-29876
Annnotations
LitCovid-PD-MONDO
{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T176","span":{"begin":51,"end":55},"obj":"Disease"},{"id":"T177","span":{"begin":61,"end":70},"obj":"Disease"},{"id":"T178","span":{"begin":364,"end":373},"obj":"Disease"},{"id":"T179","span":{"begin":436,"end":440},"obj":"Disease"},{"id":"T180","span":{"begin":602,"end":611},"obj":"Disease"},{"id":"T181","span":{"begin":616,"end":620},"obj":"Disease"},{"id":"T182","span":{"begin":696,"end":705},"obj":"Disease"},{"id":"T183","span":{"begin":738,"end":742},"obj":"Disease"},{"id":"T184","span":{"begin":874,"end":883},"obj":"Disease"},{"id":"T185","span":{"begin":915,"end":919},"obj":"Disease"},{"id":"T186","span":{"begin":925,"end":934},"obj":"Disease"},{"id":"T187","span":{"begin":1019,"end":1023},"obj":"Disease"},{"id":"T188","span":{"begin":1103,"end":1107},"obj":"Disease"},{"id":"T189","span":{"begin":1162,"end":1171},"obj":"Disease"},{"id":"T190","span":{"begin":1264,"end":1273},"obj":"Disease"},{"id":"T191","span":{"begin":1283,"end":1287},"obj":"Disease"}],"attributes":[{"id":"A176","pred":"mondo_id","subj":"T176","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A177","pred":"mondo_id","subj":"T177","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A178","pred":"mondo_id","subj":"T178","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A179","pred":"mondo_id","subj":"T179","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A180","pred":"mondo_id","subj":"T180","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A181","pred":"mondo_id","subj":"T181","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A182","pred":"mondo_id","subj":"T182","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A183","pred":"mondo_id","subj":"T183","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A184","pred":"mondo_id","subj":"T184","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A185","pred":"mondo_id","subj":"T185","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A186","pred":"mondo_id","subj":"T186","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A187","pred":"mondo_id","subj":"T187","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A188","pred":"mondo_id","subj":"T188","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A189","pred":"mondo_id","subj":"T189","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A190","pred":"mondo_id","subj":"T190","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A191","pred":"mondo_id","subj":"T191","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019, and all its mutant complexes were investigated by the MMPBSA method.48 The binding energy was partitioned into its individual components including: electrostatic, van der Waals, polar solvation, and SASA to identify important factors affecting the interface of RBD and ACE2 in all complexes. nCOV-2019 has a total binding energy of −50.22 ± 1.93 kcal/mol, whereas SARS-COV has a much higher binding energy of −18.79 ± 1.53 kcal/mol. Decomposition of binding energy to its components show that the most striking difference between nCOV-2019 and SARS-COV is the electrostatic contribution which is −746.69 ± 2.66 kcal/mol for nCOV-2019 and −600.14 ± 7.65 kcal/mol for SARS-COV. This high electrostatic contribution is compensated by a large polar solvation free energy which is 797.30 ± 3.12kcal/mol for nCOV-2019 and 659.61 ± 8.98 kcal/mol for SARS-COV. nCOV-2019 also possess a higher van der Waals (vdw) contribution (−89.93 ± 0.46 kcal/mol than SARS-COV (−70.07 ± 1.22 kcal/mol. Furthermore, the SASA contribution to binding for SARS-COV was −8.30 ± 0.15 kcal/mol and −10.58 kcal/mol for nCOV-2019. Both hydrophobic and electrostatic interactions play major roles in the higher affinity of nCOV-2019 RBD than SARS-COV RBD to ACE2."}
LitCovid-PD-CLO
{"project":"LitCovid-PD-CLO","denotations":[{"id":"T193","span":{"begin":140,"end":142},"obj":"http://purl.obolibrary.org/obo/CLO_0001382"},{"id":"T194","span":{"begin":374,"end":377},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T195","span":{"begin":378,"end":379},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T196","span":{"begin":445,"end":448},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T197","span":{"begin":449,"end":450},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T198","span":{"begin":803,"end":804},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T199","span":{"begin":948,"end":949},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019, and all its mutant complexes were investigated by the MMPBSA method.48 The binding energy was partitioned into its individual components including: electrostatic, van der Waals, polar solvation, and SASA to identify important factors affecting the interface of RBD and ACE2 in all complexes. nCOV-2019 has a total binding energy of −50.22 ± 1.93 kcal/mol, whereas SARS-COV has a much higher binding energy of −18.79 ± 1.53 kcal/mol. Decomposition of binding energy to its components show that the most striking difference between nCOV-2019 and SARS-COV is the electrostatic contribution which is −746.69 ± 2.66 kcal/mol for nCOV-2019 and −600.14 ± 7.65 kcal/mol for SARS-COV. This high electrostatic contribution is compensated by a large polar solvation free energy which is 797.30 ± 3.12kcal/mol for nCOV-2019 and 659.61 ± 8.98 kcal/mol for SARS-COV. nCOV-2019 also possess a higher van der Waals (vdw) contribution (−89.93 ± 0.46 kcal/mol than SARS-COV (−70.07 ± 1.22 kcal/mol. Furthermore, the SASA contribution to binding for SARS-COV was −8.30 ± 0.15 kcal/mol and −10.58 kcal/mol for nCOV-2019. Both hydrophobic and electrostatic interactions play major roles in the higher affinity of nCOV-2019 RBD than SARS-COV RBD to ACE2."}
LitCovid-sentences
{"project":"LitCovid-sentences","denotations":[{"id":"T181","span":{"begin":0,"end":504},"obj":"Sentence"},{"id":"T182","span":{"begin":505,"end":747},"obj":"Sentence"},{"id":"T183","span":{"begin":748,"end":1052},"obj":"Sentence"},{"id":"T184","span":{"begin":1053,"end":1172},"obj":"Sentence"},{"id":"T185","span":{"begin":1173,"end":1304},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019, and all its mutant complexes were investigated by the MMPBSA method.48 The binding energy was partitioned into its individual components including: electrostatic, van der Waals, polar solvation, and SASA to identify important factors affecting the interface of RBD and ACE2 in all complexes. nCOV-2019 has a total binding energy of −50.22 ± 1.93 kcal/mol, whereas SARS-COV has a much higher binding energy of −18.79 ± 1.53 kcal/mol. Decomposition of binding energy to its components show that the most striking difference between nCOV-2019 and SARS-COV is the electrostatic contribution which is −746.69 ± 2.66 kcal/mol for nCOV-2019 and −600.14 ± 7.65 kcal/mol for SARS-COV. This high electrostatic contribution is compensated by a large polar solvation free energy which is 797.30 ± 3.12kcal/mol for nCOV-2019 and 659.61 ± 8.98 kcal/mol for SARS-COV. nCOV-2019 also possess a higher van der Waals (vdw) contribution (−89.93 ± 0.46 kcal/mol than SARS-COV (−70.07 ± 1.22 kcal/mol. Furthermore, the SASA contribution to binding for SARS-COV was −8.30 ± 0.15 kcal/mol and −10.58 kcal/mol for nCOV-2019. Both hydrophobic and electrostatic interactions play major roles in the higher affinity of nCOV-2019 RBD than SARS-COV RBD to ACE2."}
LitCovid-PubTator
{"project":"LitCovid-PubTator","denotations":[{"id":"633","span":{"begin":31,"end":35},"obj":"Gene"},{"id":"634","span":{"begin":341,"end":345},"obj":"Gene"},{"id":"635","span":{"begin":1299,"end":1303},"obj":"Gene"},{"id":"636","span":{"begin":51,"end":59},"obj":"Species"},{"id":"637","span":{"begin":61,"end":65},"obj":"Species"},{"id":"638","span":{"begin":364,"end":368},"obj":"Species"},{"id":"639","span":{"begin":436,"end":444},"obj":"Species"},{"id":"640","span":{"begin":602,"end":606},"obj":"Species"},{"id":"641","span":{"begin":616,"end":624},"obj":"Species"},{"id":"642","span":{"begin":696,"end":700},"obj":"Species"},{"id":"643","span":{"begin":738,"end":746},"obj":"Species"},{"id":"644","span":{"begin":874,"end":878},"obj":"Species"},{"id":"645","span":{"begin":915,"end":923},"obj":"Species"},{"id":"646","span":{"begin":925,"end":929},"obj":"Species"},{"id":"647","span":{"begin":1019,"end":1027},"obj":"Species"},{"id":"648","span":{"begin":1103,"end":1111},"obj":"Species"},{"id":"649","span":{"begin":1162,"end":1166},"obj":"Species"},{"id":"650","span":{"begin":1264,"end":1268},"obj":"Species"},{"id":"651","span":{"begin":1283,"end":1291},"obj":"Species"}],"attributes":[{"id":"A633","pred":"tao:has_database_id","subj":"633","obj":"Gene:59272"},{"id":"A634","pred":"tao:has_database_id","subj":"634","obj":"Gene:59272"},{"id":"A635","pred":"tao:has_database_id","subj":"635","obj":"Gene:59272"},{"id":"A636","pred":"tao:has_database_id","subj":"636","obj":"Tax:694009"},{"id":"A637","pred":"tao:has_database_id","subj":"637","obj":"Tax:2697049"},{"id":"A638","pred":"tao:has_database_id","subj":"638","obj":"Tax:2697049"},{"id":"A639","pred":"tao:has_database_id","subj":"639","obj":"Tax:694009"},{"id":"A640","pred":"tao:has_database_id","subj":"640","obj":"Tax:2697049"},{"id":"A641","pred":"tao:has_database_id","subj":"641","obj":"Tax:694009"},{"id":"A642","pred":"tao:has_database_id","subj":"642","obj":"Tax:2697049"},{"id":"A643","pred":"tao:has_database_id","subj":"643","obj":"Tax:694009"},{"id":"A644","pred":"tao:has_database_id","subj":"644","obj":"Tax:2697049"},{"id":"A645","pred":"tao:has_database_id","subj":"645","obj":"Tax:694009"},{"id":"A646","pred":"tao:has_database_id","subj":"646","obj":"Tax:2697049"},{"id":"A647","pred":"tao:has_database_id","subj":"647","obj":"Tax:694009"},{"id":"A648","pred":"tao:has_database_id","subj":"648","obj":"Tax:694009"},{"id":"A649","pred":"tao:has_database_id","subj":"649","obj":"Tax:2697049"},{"id":"A650","pred":"tao:has_database_id","subj":"650","obj":"Tax:2697049"},{"id":"A651","pred":"tao:has_database_id","subj":"651","obj":"Tax:694009"}],"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":"The binding energetics between ACE2 and the RBD of SARS-COV, nCOV-2019, and all its mutant complexes were investigated by the MMPBSA method.48 The binding energy was partitioned into its individual components including: electrostatic, van der Waals, polar solvation, and SASA to identify important factors affecting the interface of RBD and ACE2 in all complexes. nCOV-2019 has a total binding energy of −50.22 ± 1.93 kcal/mol, whereas SARS-COV has a much higher binding energy of −18.79 ± 1.53 kcal/mol. Decomposition of binding energy to its components show that the most striking difference between nCOV-2019 and SARS-COV is the electrostatic contribution which is −746.69 ± 2.66 kcal/mol for nCOV-2019 and −600.14 ± 7.65 kcal/mol for SARS-COV. This high electrostatic contribution is compensated by a large polar solvation free energy which is 797.30 ± 3.12kcal/mol for nCOV-2019 and 659.61 ± 8.98 kcal/mol for SARS-COV. nCOV-2019 also possess a higher van der Waals (vdw) contribution (−89.93 ± 0.46 kcal/mol than SARS-COV (−70.07 ± 1.22 kcal/mol. Furthermore, the SASA contribution to binding for SARS-COV was −8.30 ± 0.15 kcal/mol and −10.58 kcal/mol for nCOV-2019. Both hydrophobic and electrostatic interactions play major roles in the higher affinity of nCOV-2019 RBD than SARS-COV RBD to ACE2."}