PMC:7605337 / 20813-21677 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T49","span":{"begin":731,"end":739},"obj":"Body_part"}],"attributes":[{"id":"A49","pred":"fma_id","subj":"T49","obj":"http://purl.org/sig/ont/fma/fma13478"}],"text":"The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T126","span":{"begin":23,"end":32},"obj":"Disease"},{"id":"T127","span":{"begin":67,"end":76},"obj":"Disease"}],"attributes":[{"id":"A126","pred":"mondo_id","subj":"T126","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"},{"id":"A127","pred":"mondo_id","subj":"T127","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T131","span":{"begin":232,"end":233},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T132","span":{"begin":330,"end":331},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T133","span":{"begin":346,"end":347},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T134","span":{"begin":426,"end":427},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T135","span":{"begin":449,"end":450},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T136","span":{"begin":538,"end":539},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T137","span":{"begin":561,"end":562},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T138","span":{"begin":605,"end":606},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T139","span":{"begin":627,"end":628},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T140","span":{"begin":702,"end":705},"obj":"http://purl.obolibrary.org/obo/CLO_0001236"},{"id":"T141","span":{"begin":861,"end":863},"obj":"http://purl.obolibrary.org/obo/CLO_0050050"}],"text":"The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T7","span":{"begin":54,"end":63},"obj":"http://purl.obolibrary.org/obo/GO_0007610"},{"id":"T8","span":{"begin":524,"end":532},"obj":"http://purl.obolibrary.org/obo/GO_0007610"}],"text":"The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1."}

{"project":"LitCovid-sentences","denotations":[{"id":"T110","span":{"begin":0,"end":80},"obj":"Sentence"},{"id":"T111","span":{"begin":81,"end":222},"obj":"Sentence"},{"id":"T112","span":{"begin":223,"end":274},"obj":"Sentence"},{"id":"T113","span":{"begin":275,"end":362},"obj":"Sentence"},{"id":"T114","span":{"begin":363,"end":475},"obj":"Sentence"},{"id":"T115","span":{"begin":476,"end":563},"obj":"Sentence"},{"id":"T116","span":{"begin":564,"end":629},"obj":"Sentence"},{"id":"T117","span":{"begin":630,"end":706},"obj":"Sentence"},{"id":"T118","span":{"begin":707,"end":809},"obj":"Sentence"},{"id":"T119","span":{"begin":810,"end":864},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"The RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1."}

{"project":"LitCovid-PubTator","denotations":[{"id":"466","span":{"begin":23,"end":27},"obj":"Species"},{"id":"467","span":{"begin":67,"end":71},"obj":"Species"}],"attributes":[{"id":"A466","pred":"tao:has_database_id","subj":"466","obj":"Tax:2697049"},{"id":"A467","pred":"tao:has_database_id","subj":"467","obj":"Tax:2697049"}],"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 RMSD plots for the nCOV-2019 mutants show similar behaviors to nCOV-2019-wt. In most of the variants, the RMSD is very stable during the 300 ns simulation which shows the great tolerance of the interface for mutations. However, a few mutations showed some RMSD variance. In mutation Y489A, the RMSD increases from 1.37 ± 0.21 Å to1.88 ± 0.16 Å after 2000 ns. Mutation Y505A resulted in an increase in RMSD up to 100 ns to a value to 1.98 ± 0.20 Å and decreased afterward. The RMSD for mutation N487A shows an increasing behavior with a value of 2.10 ± 0.23 Å. Mutations N439K, V483A, and V483F showed a stable RMSD of ∼1.5 Å. For mutations T478I, G476S, S494P, and A475V, the RMSD increases up to ∼2 Å. These variations in the backbone RMSD show the involvement of these residues in the complex stability. RMSD plots for other mutations are shown in Figure S1."}