PMC:7189872 / 8087-8609 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"131","span":{"begin":239,"end":246},"obj":"Species"},{"id":"132","span":{"begin":373,"end":379},"obj":"Chemical"},{"id":"133","span":{"begin":202,"end":219},"obj":"Disease"}],"attributes":[{"id":"A131","pred":"tao:has_database_id","subj":"131","obj":"Tax:342041"},{"id":"A132","pred":"tao:has_database_id","subj":"132","obj":"MESH:D002244"},{"id":"A133","pred":"tao:has_database_id","subj":"133","obj":"MESH:D009436"}],"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":"Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17]."}

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T65","span":{"begin":94,"end":105},"obj":"Body_part"},{"id":"T66","span":{"begin":340,"end":342},"obj":"Body_part"}],"attributes":[{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A66","pred":"fma_id","subj":"T66","obj":"http://purl.org/sig/ont/fma/fma66595"}],"text":"Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17]."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T67","span":{"begin":120,"end":122},"obj":"http://purl.obolibrary.org/obo/CLO_0008491"},{"id":"T68","span":{"begin":217,"end":219},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T69","span":{"begin":280,"end":282},"obj":"http://purl.obolibrary.org/obo/CLO_0008491"},{"id":"T70","span":{"begin":340,"end":342},"obj":"http://purl.obolibrary.org/obo/CLO_0001562"},{"id":"T71","span":{"begin":340,"end":342},"obj":"http://purl.obolibrary.org/obo/CLO_0001563"},{"id":"T72","span":{"begin":386,"end":387},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T73","span":{"begin":450,"end":451},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T74","span":{"begin":460,"end":462},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T75","span":{"begin":511,"end":516},"obj":"http://purl.obolibrary.org/obo/UBERON_0007688"}],"text":"Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17]."}

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T55","span":{"begin":94,"end":105},"obj":"Chemical"},{"id":"T56","span":{"begin":94,"end":99},"obj":"Chemical"},{"id":"T57","span":{"begin":100,"end":105},"obj":"Chemical"},{"id":"T58","span":{"begin":217,"end":219},"obj":"Chemical"},{"id":"T59","span":{"begin":241,"end":246},"obj":"Chemical"},{"id":"T60","span":{"begin":367,"end":372},"obj":"Chemical"},{"id":"T61","span":{"begin":373,"end":379},"obj":"Chemical"},{"id":"T63","span":{"begin":380,"end":385},"obj":"Chemical"},{"id":"T64","span":{"begin":460,"end":462},"obj":"Chemical"}],"attributes":[{"id":"A55","pred":"chebi_id","subj":"T55","obj":"http://purl.obolibrary.org/obo/CHEBI_33709"},{"id":"A56","pred":"chebi_id","subj":"T56","obj":"http://purl.obolibrary.org/obo/CHEBI_46882"},{"id":"A57","pred":"chebi_id","subj":"T57","obj":"http://purl.obolibrary.org/obo/CHEBI_37527"},{"id":"A58","pred":"chebi_id","subj":"T58","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"},{"id":"A59","pred":"chebi_id","subj":"T59","obj":"http://purl.obolibrary.org/obo/CHEBI_30216"},{"id":"A60","pred":"chebi_id","subj":"T60","obj":"http://purl.obolibrary.org/obo/CHEBI_30216"},{"id":"A61","pred":"chebi_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/CHEBI_27594"},{"id":"A62","pred":"chebi_id","subj":"T61","obj":"http://purl.obolibrary.org/obo/CHEBI_33415"},{"id":"A63","pred":"chebi_id","subj":"T63","obj":"http://purl.obolibrary.org/obo/CHEBI_33250"},{"id":"A64","pred":"chebi_id","subj":"T64","obj":"http://purl.obolibrary.org/obo/CHEBI_74699"}],"text":"Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17]."}

{"project":"LitCovid-sentences","denotations":[{"id":"T65","span":{"begin":0,"end":164},"obj":"Sentence"},{"id":"T66","span":{"begin":165,"end":275},"obj":"Sentence"},{"id":"T67","span":{"begin":276,"end":522},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17]."}

{"project":"LitCovid-PMC-OGER-BB","denotations":[{"id":"T157","span":{"begin":66,"end":72},"obj":"CHEBI:33250;CHEBI:33250"},{"id":"T158","span":{"begin":380,"end":385},"obj":"CHEBI:33250;CHEBI:33250"},{"id":"T159","span":{"begin":420,"end":428},"obj":"BV_9"},{"id":"T95805","span":{"begin":66,"end":72},"obj":"CHEBI:33250;CHEBI:33250"},{"id":"T80172","span":{"begin":380,"end":385},"obj":"CHEBI:33250;CHEBI:33250"},{"id":"T29153","span":{"begin":420,"end":428},"obj":"BV_9"}],"text":"Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17]."}

{"project":"2_test","denotations":[{"id":"32352026-22437851-47638073","span":{"begin":518,"end":520},"obj":"22437851"},{"id":"T52774","span":{"begin":518,"end":520},"obj":"22437851"}],"text":"Molecular dynamics study was conducted to analyze RMSD values and atomic fluctuations for all amino acids under the 100 ps time frame by deploying the MDWeb server. MDWeb server was deployed to analyze Coarse grained MD Brownian dynamics (C-alpha) with specifications → Time: 100 ps, output frequency (steps) = 10, force constant (kcal/mol Ǻ2) = 40, distance between alpha carbon atoms(Ǻ) = 3.8 for both the interacting epitopes, and it was based on a GROMACS MD setup with solvation using an Amber-99sb* force-field [17]."}