PMC:7544943 / 13052-15030 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T15","span":{"begin":1735,"end":1741},"obj":"Body_part"}],"attributes":[{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma23463"}],"text":"2.4. Molecular dynamics (MD) simulation study\nTo verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015). The CHARMM36 forcefield (Huang \u0026 MacKerell, 2013) was used for the simulation of the systems. The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe \u0026 MacKerell, 2012). A dodecahedron simulation box filled with TIP3P water model (Price \u0026 Brooks, 2004) was prepared. Counter ions were added to maintain the electrical neutrality of the system. The systems were kept at a buffer concentration of 0.15 M. Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm. Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run. After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble. For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used. Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello \u0026 Rahman, 1981) with isotropic rescaling were used, respectively. The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps. The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools. The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs. The data were exported to origin 9.0 and plotted for further analysis purposes."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T41","span":{"begin":114,"end":122},"obj":"Disease"},{"id":"T42","span":{"begin":138,"end":146},"obj":"Disease"},{"id":"T43","span":{"begin":1159,"end":1162},"obj":"Disease"}],"attributes":[{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A42","pred":"mondo_id","subj":"T42","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A43","pred":"mondo_id","subj":"T43","obj":"http://purl.obolibrary.org/obo/MONDO_0020074"}],"text":"2.4. Molecular dynamics (MD) simulation study\nTo verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015). The CHARMM36 forcefield (Huang \u0026 MacKerell, 2013) was used for the simulation of the systems. The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe \u0026 MacKerell, 2012). A dodecahedron simulation box filled with TIP3P water model (Price \u0026 Brooks, 2004) was prepared. Counter ions were added to maintain the electrical neutrality of the system. The systems were kept at a buffer concentration of 0.15 M. Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm. Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run. After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble. For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used. Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello \u0026 Rahman, 1981) with isotropic rescaling were used, respectively. The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps. The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools. The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs. The data were exported to origin 9.0 and plotted for further analysis purposes."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T62","span":{"begin":26,"end":28},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T63","span":{"begin":172,"end":174},"obj":"http://purl.obolibrary.org/obo/CLO_0007622"},{"id":"T64","span":{"begin":527,"end":528},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T65","span":{"begin":726,"end":727},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T66","span":{"begin":933,"end":935},"obj":"http://purl.obolibrary.org/obo/CLO_0008491"},{"id":"T67","span":{"begin":1028,"end":1029},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T68","span":{"begin":1579,"end":1581},"obj":"http://purl.obolibrary.org/obo/CLO_0008491"}],"text":"2.4. Molecular dynamics (MD) simulation study\nTo verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015). The CHARMM36 forcefield (Huang \u0026 MacKerell, 2013) was used for the simulation of the systems. The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe \u0026 MacKerell, 2012). A dodecahedron simulation box filled with TIP3P water model (Price \u0026 Brooks, 2004) was prepared. Counter ions were added to maintain the electrical neutrality of the system. The systems were kept at a buffer concentration of 0.15 M. Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm. Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run. After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble. For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used. Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello \u0026 Rahman, 1981) with isotropic rescaling were used, respectively. The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps. The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools. The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs. The data were exported to origin 9.0 and plotted for further analysis purposes."}

{"project":"LitCovid-PubTator","denotations":[{"id":"269","span":{"begin":263,"end":267},"obj":"Gene"},{"id":"270","span":{"begin":149,"end":153},"obj":"Gene"},{"id":"271","span":{"begin":114,"end":124},"obj":"Species"},{"id":"272","span":{"begin":138,"end":148},"obj":"Species"},{"id":"273","span":{"begin":245,"end":258},"obj":"Chemical"},{"id":"274","span":{"begin":575,"end":580},"obj":"Chemical"},{"id":"275","span":{"begin":1716,"end":1724},"obj":"Chemical"}],"attributes":[{"id":"A269","pred":"tao:has_database_id","subj":"269","obj":"Gene:8673700"},{"id":"A270","pred":"tao:has_database_id","subj":"270","obj":"Gene:8673700"},{"id":"A271","pred":"tao:has_database_id","subj":"271","obj":"Tax:2697049"},{"id":"A272","pred":"tao:has_database_id","subj":"272","obj":"Tax:2697049"},{"id":"A274","pred":"tao:has_database_id","subj":"274","obj":"MESH:D014867"},{"id":"A275","pred":"tao:has_database_id","subj":"275","obj":"MESH:D006859"}],"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":"2.4. Molecular dynamics (MD) simulation study\nTo verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015). The CHARMM36 forcefield (Huang \u0026 MacKerell, 2013) was used for the simulation of the systems. The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe \u0026 MacKerell, 2012). A dodecahedron simulation box filled with TIP3P water model (Price \u0026 Brooks, 2004) was prepared. Counter ions were added to maintain the electrical neutrality of the system. The systems were kept at a buffer concentration of 0.15 M. Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm. Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run. After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble. For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used. Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello \u0026 Rahman, 1981) with isotropic rescaling were used, respectively. The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps. The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools. The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs. The data were exported to origin 9.0 and plotted for further analysis purposes."}

{"project":"LitCovid-sentences","denotations":[{"id":"T125","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T126","span":{"begin":6,"end":46},"obj":"Sentence"},{"id":"T127","span":{"begin":47,"end":322},"obj":"Sentence"},{"id":"T128","span":{"begin":323,"end":416},"obj":"Sentence"},{"id":"T129","span":{"begin":417,"end":526},"obj":"Sentence"},{"id":"T130","span":{"begin":527,"end":623},"obj":"Sentence"},{"id":"T131","span":{"begin":624,"end":700},"obj":"Sentence"},{"id":"T132","span":{"begin":701,"end":759},"obj":"Sentence"},{"id":"T133","span":{"begin":760,"end":861},"obj":"Sentence"},{"id":"T134","span":{"begin":862,"end":1002},"obj":"Sentence"},{"id":"T135","span":{"begin":1003,"end":1095},"obj":"Sentence"},{"id":"T136","span":{"begin":1096,"end":1258},"obj":"Sentence"},{"id":"T137","span":{"begin":1259,"end":1489},"obj":"Sentence"},{"id":"T138","span":{"begin":1490,"end":1582},"obj":"Sentence"},{"id":"T139","span":{"begin":1583,"end":1788},"obj":"Sentence"},{"id":"T140","span":{"begin":1789,"end":1898},"obj":"Sentence"},{"id":"T141","span":{"begin":1899,"end":1978},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"2.4. Molecular dynamics (MD) simulation study\nTo verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015). The CHARMM36 forcefield (Huang \u0026 MacKerell, 2013) was used for the simulation of the systems. The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe \u0026 MacKerell, 2012). A dodecahedron simulation box filled with TIP3P water model (Price \u0026 Brooks, 2004) was prepared. Counter ions were added to maintain the electrical neutrality of the system. The systems were kept at a buffer concentration of 0.15 M. Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm. Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run. After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble. For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used. Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello \u0026 Rahman, 1981) with isotropic rescaling were used, respectively. The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps. The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools. The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs. The data were exported to origin 9.0 and plotted for further analysis purposes."}

{"project":"2_test","denotations":[{"id":"32938313-23832629-56197381","span":{"begin":367,"end":371},"obj":"23832629"},{"id":"32938313-23146088-56197382","span":{"begin":520,"end":524},"obj":"23146088"},{"id":"32938313-15549884-56197383","span":{"begin":604,"end":608},"obj":"15549884"}],"text":"2.4. Molecular dynamics (MD) simulation study\nTo verify the stability of the complex and interaction dynamics of SARS-CoV-2 RBD Spro and SARS-CoV-2 Mpro, we performed the MD simulation study of the two complexes with the highest docking score (Spro-Piperine and Mpro-Piperine), using GROMACS-5.1.5 (Abraham et al., 2015). The CHARMM36 forcefield (Huang \u0026 MacKerell, 2013) was used for the simulation of the systems. The topology parameters for the ligand molecule were obtained from CGenFF (Vanommeslaeghe \u0026 MacKerell, 2012). A dodecahedron simulation box filled with TIP3P water model (Price \u0026 Brooks, 2004) was prepared. Counter ions were added to maintain the electrical neutrality of the system. The systems were kept at a buffer concentration of 0.15 M. Then, the build systems were energy minimized with 50,000 steps using the steepest descent algorithm. Then the systems were equilibrated under NVT and NPT ensembles for 100 ps at 300 K temperature and 1 atm pressure before the production run. After the equilibration, a production run of 100 ns was incorporated under the NPT ensemble. For long-range electrostatic interaction, particle mesh Ewald (PME) (Darden et al., 1993) and for van der Waals interactions, the force-switching scheme was used. Besides, for temperature and pressure coupling, the Berendsen thermostat (Berendsen et al., 1984) with velocity rescaling and Parrinello-Rahman barostat (Parrinello \u0026 Rahman, 1981) with isotropic rescaling were used, respectively. The simulation time step was set to 2 fs, and the trajectories were recorded at every 10 ps. The simulation data were analysed by analysing the root mean square deviation (RMSD), root mean square fluctuation (RMSF), number of hydrogen bonds and radius of gyration (Rg) using Gromacs analysis tools. The principal component analysis (PCA) was performed using the g_covar, g_anaeig and g_sham tools of Gromacs. The data were exported to origin 9.0 and plotted for further analysis purposes."}