PMC:7605337 / 15547-16428 JSONTXT

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T105","span":{"begin":487,"end":491},"obj":"Disease"},{"id":"T106","span":{"begin":500,"end":509},"obj":"Disease"}],"attributes":[{"id":"A105","pred":"mondo_id","subj":"T105","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A106","pred":"mondo_id","subj":"T106","obj":"http://purl.obolibrary.org/obo/MONDO_0100096"}],"text":"In the production run, harmonic restraints were removed and all the systems were simulated using a NPT ensemble where the pressure was maintained at 1 bar using the Parrinello-Rahman barostat40 with a compressibility of 4.5 × 10–5bar–1 and a coupling constant of 0.5 ps. It is important to note that the Berendsen barostat was only used for the equilibration step as it was shown that this barostat can cause unrealistic temperature gradients.41 The production run lasted for 500 ns for SARS-COV and nCOV-2019 complexes and 300 ns for all the mutants with a 2 fs timestep and the particle-mesh Ewald42 for long range electrostatic interactions using the GROMACS 2018.3 package.43 All mutant systems were constructed as described before and ran for 300 ns of production run. In addition, the simulation time for a few mutants (Y449A, T478I, Y489A, and S494P) was extended to 500 ns."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T101","span":{"begin":97,"end":98},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T102","span":{"begin":146,"end":150},"obj":"http://purl.obolibrary.org/obo/CLO_0001757"},{"id":"T103","span":{"begin":199,"end":200},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T104","span":{"begin":240,"end":241},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T105","span":{"begin":267,"end":269},"obj":"http://purl.obolibrary.org/obo/CLO_0008491"},{"id":"T106","span":{"begin":443,"end":445},"obj":"http://purl.obolibrary.org/obo/CLO_0053794"},{"id":"T107","span":{"begin":556,"end":559},"obj":"http://purl.obolibrary.org/obo/CLO_0001562"},{"id":"T108","span":{"begin":556,"end":559},"obj":"http://purl.obolibrary.org/obo/CLO_0001563"},{"id":"T109","span":{"begin":811,"end":812},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"In the production run, harmonic restraints were removed and all the systems were simulated using a NPT ensemble where the pressure was maintained at 1 bar using the Parrinello-Rahman barostat40 with a compressibility of 4.5 × 10–5bar–1 and a coupling constant of 0.5 ps. It is important to note that the Berendsen barostat was only used for the equilibration step as it was shown that this barostat can cause unrealistic temperature gradients.41 The production run lasted for 500 ns for SARS-COV and nCOV-2019 complexes and 300 ns for all the mutants with a 2 fs timestep and the particle-mesh Ewald42 for long range electrostatic interactions using the GROMACS 2018.3 package.43 All mutant systems were constructed as described before and ran for 300 ns of production run. In addition, the simulation time for a few mutants (Y449A, T478I, Y489A, and S494P) was extended to 500 ns."}

{"project":"LitCovid-sentences","denotations":[{"id":"T81","span":{"begin":0,"end":270},"obj":"Sentence"},{"id":"T82","span":{"begin":271,"end":773},"obj":"Sentence"},{"id":"T83","span":{"begin":774,"end":881},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In the production run, harmonic restraints were removed and all the systems were simulated using a NPT ensemble where the pressure was maintained at 1 bar using the Parrinello-Rahman barostat40 with a compressibility of 4.5 × 10–5bar–1 and a coupling constant of 0.5 ps. It is important to note that the Berendsen barostat was only used for the equilibration step as it was shown that this barostat can cause unrealistic temperature gradients.41 The production run lasted for 500 ns for SARS-COV and nCOV-2019 complexes and 300 ns for all the mutants with a 2 fs timestep and the particle-mesh Ewald42 for long range electrostatic interactions using the GROMACS 2018.3 package.43 All mutant systems were constructed as described before and ran for 300 ns of production run. In addition, the simulation time for a few mutants (Y449A, T478I, Y489A, and S494P) was extended to 500 ns."}

{"project":"LitCovid-PubTator","denotations":[{"id":"411","span":{"begin":654,"end":661},"obj":"Gene"},{"id":"412","span":{"begin":487,"end":495},"obj":"Species"},{"id":"413","span":{"begin":500,"end":504},"obj":"Species"}],"attributes":[{"id":"A411","pred":"tao:has_database_id","subj":"411","obj":"Gene:4082"},{"id":"A412","pred":"tao:has_database_id","subj":"412","obj":"Tax:694009"},{"id":"A413","pred":"tao:has_database_id","subj":"413","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":"In the production run, harmonic restraints were removed and all the systems were simulated using a NPT ensemble where the pressure was maintained at 1 bar using the Parrinello-Rahman barostat40 with a compressibility of 4.5 × 10–5bar–1 and a coupling constant of 0.5 ps. It is important to note that the Berendsen barostat was only used for the equilibration step as it was shown that this barostat can cause unrealistic temperature gradients.41 The production run lasted for 500 ns for SARS-COV and nCOV-2019 complexes and 300 ns for all the mutants with a 2 fs timestep and the particle-mesh Ewald42 for long range electrostatic interactions using the GROMACS 2018.3 package.43 All mutant systems were constructed as described before and ran for 300 ns of production run. In addition, the simulation time for a few mutants (Y449A, T478I, Y489A, and S494P) was extended to 500 ns."}