PMC:7605337 / 40503-41467 JSONTXT

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T274","span":{"begin":113,"end":122},"obj":"Disease"},{"id":"T275","span":{"begin":144,"end":148},"obj":"Disease"},{"id":"T276","span":{"begin":199,"end":208},"obj":"Disease"},{"id":"T277","span":{"begin":317,"end":326},"obj":"Disease"},{"id":"T278","span":{"begin":328,"end":332},"obj":"Disease"},{"id":"T279","span":{"begin":726,"end":735},"obj":"Disease"},{"id":"T280","span":{"begin":797,"end":806},"obj":"Disease"},{"id":"T281","span":{"begin":933,"end":948},"obj":"Disease"},{"id":"T282","span":{"begin":939,"end":948},"obj":"Disease"}],"attributes":[{"id":"A274","pred":"mondo_id","subj":"T274","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A275","pred":"mondo_id","subj":"T275","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A276","pred":"mondo_id","subj":"T276","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A277","pred":"mondo_id","subj":"T277","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A278","pred":"mondo_id","subj":"T278","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A279","pred":"mondo_id","subj":"T279","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A280","pred":"mondo_id","subj":"T280","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"},{"id":"A281","pred":"mondo_id","subj":"T281","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"},{"id":"A282","pred":"mondo_id","subj":"T282","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"In this work, we preformed MD simulations to unveil the detailed molecular mechanism for the receptor binding of nCOV-2019 and compared it with SARS-COV. The role of key residues at the interface of nCOV-2019 with ACE2 was investigated by computational ala-scanning. A rigorous 500 ns MD simulation was performed for nCOV-2019, SARS-COV, and few mutants (Y449, T478I, Y489A, and S494P) as well as 300 ns MD simulation on each mutant. These simulations aid in understanding the dynamic role of RBD/ACE2 interface residues and estimating the binding free energy of these variants, which shed light on crucial residues for the RBD/ACE2 complex stability. Moreover, numerous mutations have been identified in the RBD of different nCOV-2019 strains from all over the world not known to be critical for infection.54 The effect of these mutations on the stability of the RBD/ACE2 complex was investigated to shed light on their role in the viral infection of coronavirus."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T248","span":{"begin":27,"end":29},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T249","span":{"begin":267,"end":268},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T250","span":{"begin":285,"end":287},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T251","span":{"begin":404,"end":406},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"}],"text":"In this work, we preformed MD simulations to unveil the detailed molecular mechanism for the receptor binding of nCOV-2019 and compared it with SARS-COV. The role of key residues at the interface of nCOV-2019 with ACE2 was investigated by computational ala-scanning. A rigorous 500 ns MD simulation was performed for nCOV-2019, SARS-COV, and few mutants (Y449, T478I, Y489A, and S494P) as well as 300 ns MD simulation on each mutant. These simulations aid in understanding the dynamic role of RBD/ACE2 interface residues and estimating the binding free energy of these variants, which shed light on crucial residues for the RBD/ACE2 complex stability. Moreover, numerous mutations have been identified in the RBD of different nCOV-2019 strains from all over the world not known to be critical for infection.54 The effect of these mutations on the stability of the RBD/ACE2 complex was investigated to shed light on their role in the viral infection of coronavirus."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T125","span":{"begin":27,"end":29},"obj":"Chemical"},{"id":"T126","span":{"begin":285,"end":287},"obj":"Chemical"},{"id":"T127","span":{"begin":404,"end":406},"obj":"Chemical"}],"attributes":[{"id":"A125","pred":"chebi_id","subj":"T125","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A126","pred":"chebi_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A127","pred":"chebi_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"}],"text":"In this work, we preformed MD simulations to unveil the detailed molecular mechanism for the receptor binding of nCOV-2019 and compared it with SARS-COV. The role of key residues at the interface of nCOV-2019 with ACE2 was investigated by computational ala-scanning. A rigorous 500 ns MD simulation was performed for nCOV-2019, SARS-COV, and few mutants (Y449, T478I, Y489A, and S494P) as well as 300 ns MD simulation on each mutant. These simulations aid in understanding the dynamic role of RBD/ACE2 interface residues and estimating the binding free energy of these variants, which shed light on crucial residues for the RBD/ACE2 complex stability. Moreover, numerous mutations have been identified in the RBD of different nCOV-2019 strains from all over the world not known to be critical for infection.54 The effect of these mutations on the stability of the RBD/ACE2 complex was investigated to shed light on their role in the viral infection of coronavirus."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T12","span":{"begin":933,"end":948},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"In this work, we preformed MD simulations to unveil the detailed molecular mechanism for the receptor binding of nCOV-2019 and compared it with SARS-COV. The role of key residues at the interface of nCOV-2019 with ACE2 was investigated by computational ala-scanning. A rigorous 500 ns MD simulation was performed for nCOV-2019, SARS-COV, and few mutants (Y449, T478I, Y489A, and S494P) as well as 300 ns MD simulation on each mutant. These simulations aid in understanding the dynamic role of RBD/ACE2 interface residues and estimating the binding free energy of these variants, which shed light on crucial residues for the RBD/ACE2 complex stability. Moreover, numerous mutations have been identified in the RBD of different nCOV-2019 strains from all over the world not known to be critical for infection.54 The effect of these mutations on the stability of the RBD/ACE2 complex was investigated to shed light on their role in the viral infection of coronavirus."}

{"project":"LitCovid-sentences","denotations":[{"id":"T278","span":{"begin":0,"end":153},"obj":"Sentence"},{"id":"T279","span":{"begin":154,"end":266},"obj":"Sentence"},{"id":"T280","span":{"begin":267,"end":433},"obj":"Sentence"},{"id":"T281","span":{"begin":434,"end":651},"obj":"Sentence"},{"id":"T282","span":{"begin":652,"end":964},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In this work, we preformed MD simulations to unveil the detailed molecular mechanism for the receptor binding of nCOV-2019 and compared it with SARS-COV. The role of key residues at the interface of nCOV-2019 with ACE2 was investigated by computational ala-scanning. A rigorous 500 ns MD simulation was performed for nCOV-2019, SARS-COV, and few mutants (Y449, T478I, Y489A, and S494P) as well as 300 ns MD simulation on each mutant. These simulations aid in understanding the dynamic role of RBD/ACE2 interface residues and estimating the binding free energy of these variants, which shed light on crucial residues for the RBD/ACE2 complex stability. Moreover, numerous mutations have been identified in the RBD of different nCOV-2019 strains from all over the world not known to be critical for infection.54 The effect of these mutations on the stability of the RBD/ACE2 complex was investigated to shed light on their role in the viral infection of coronavirus."}

{"project":"LitCovid-PubTator","denotations":[{"id":"1002","span":{"begin":214,"end":218},"obj":"Gene"},{"id":"1003","span":{"begin":497,"end":501},"obj":"Gene"},{"id":"1004","span":{"begin":628,"end":632},"obj":"Gene"},{"id":"1005","span":{"begin":868,"end":872},"obj":"Gene"},{"id":"1006","span":{"begin":113,"end":117},"obj":"Species"},{"id":"1007","span":{"begin":144,"end":152},"obj":"Species"},{"id":"1008","span":{"begin":199,"end":203},"obj":"Species"},{"id":"1009","span":{"begin":317,"end":321},"obj":"Species"},{"id":"1010","span":{"begin":328,"end":336},"obj":"Species"},{"id":"1011","span":{"begin":726,"end":730},"obj":"Species"},{"id":"1012","span":{"begin":952,"end":963},"obj":"Species"},{"id":"1013","span":{"begin":253,"end":256},"obj":"Chemical"},{"id":"1014","span":{"begin":797,"end":806},"obj":"Disease"},{"id":"1015","span":{"begin":933,"end":948},"obj":"Disease"}],"attributes":[{"id":"A1002","pred":"tao:has_database_id","subj":"1002","obj":"Gene:59272"},{"id":"A1003","pred":"tao:has_database_id","subj":"1003","obj":"Gene:59272"},{"id":"A1004","pred":"tao:has_database_id","subj":"1004","obj":"Gene:59272"},{"id":"A1005","pred":"tao:has_database_id","subj":"1005","obj":"Gene:59272"},{"id":"A1006","pred":"tao:has_database_id","subj":"1006","obj":"Tax:2697049"},{"id":"A1007","pred":"tao:has_database_id","subj":"1007","obj":"Tax:694009"},{"id":"A1008","pred":"tao:has_database_id","subj":"1008","obj":"Tax:2697049"},{"id":"A1009","pred":"tao:has_database_id","subj":"1009","obj":"Tax:2697049"},{"id":"A1010","pred":"tao:has_database_id","subj":"1010","obj":"Tax:694009"},{"id":"A1011","pred":"tao:has_database_id","subj":"1011","obj":"Tax:2697049"},{"id":"A1012","pred":"tao:has_database_id","subj":"1012","obj":"Tax:11118"},{"id":"A1013","pred":"tao:has_database_id","subj":"1013","obj":"MESH:D000409"},{"id":"A1014","pred":"tao:has_database_id","subj":"1014","obj":"MESH:D007239"},{"id":"A1015","pred":"tao:has_database_id","subj":"1015","obj":"MESH:D001102"}],"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":"In this work, we preformed MD simulations to unveil the detailed molecular mechanism for the receptor binding of nCOV-2019 and compared it with SARS-COV. The role of key residues at the interface of nCOV-2019 with ACE2 was investigated by computational ala-scanning. A rigorous 500 ns MD simulation was performed for nCOV-2019, SARS-COV, and few mutants (Y449, T478I, Y489A, and S494P) as well as 300 ns MD simulation on each mutant. These simulations aid in understanding the dynamic role of RBD/ACE2 interface residues and estimating the binding free energy of these variants, which shed light on crucial residues for the RBD/ACE2 complex stability. Moreover, numerous mutations have been identified in the RBD of different nCOV-2019 strains from all over the world not known to be critical for infection.54 The effect of these mutations on the stability of the RBD/ACE2 complex was investigated to shed light on their role in the viral infection of coronavirus."}