PMC:7544934 / 11171-12712 JSONTXT

{"project":"LitCovid-PubTator","denotations":[{"id":"271","span":{"begin":77,"end":81},"obj":"Gene"},{"id":"272","span":{"begin":933,"end":936},"obj":"Gene"},{"id":"273","span":{"begin":504,"end":509},"obj":"Chemical"},{"id":"274","span":{"begin":523,"end":528},"obj":"Chemical"},{"id":"275","span":{"begin":595,"end":599},"obj":"Chemical"},{"id":"276","span":{"begin":761,"end":769},"obj":"Chemical"},{"id":"277","span":{"begin":1363,"end":1371},"obj":"Chemical"},{"id":"278","span":{"begin":107,"end":115},"obj":"Disease"},{"id":"279","span":{"begin":369,"end":375},"obj":"Disease"}],"attributes":[{"id":"A271","pred":"tao:has_database_id","subj":"271","obj":"Gene:59272"},{"id":"A272","pred":"tao:has_database_id","subj":"272","obj":"Gene:472"},{"id":"A273","pred":"tao:has_database_id","subj":"273","obj":"MESH:D014867"},{"id":"A274","pred":"tao:has_database_id","subj":"274","obj":"MESH:D014867"},{"id":"A275","pred":"tao:has_database_id","subj":"275","obj":"MESH:D012965"},{"id":"A276","pred":"tao:has_database_id","subj":"276","obj":"MESH:D006859"},{"id":"A277","pred":"tao:has_database_id","subj":"277","obj":"MESH:D006859"},{"id":"A278","pred":"tao:has_database_id","subj":"278","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":"To study the dynamic behavior, stability, and conformational flexibility RBD-ACE2- naltrexone complex, all-atoms MD simulations were performed as reported previously (Dehury et al., 2014; 2017; Girdhar et al., 2019). CHARMM36 force fields were used for topology building of protein in GROMACSv2019.4 package (Abraham et al., 2015). The ligand topology was derived from CHARMM General Force Field (https://cgenff.umaryland.edu/) (Vanommeslaeghe and MacKerell, 2012). The structure was solvated in a cubic water box in TIP3P water model. The system charge was electro-neutralized by adding 0.15 M NaCl to the solvated system. To eliminate bad contacts in the complex system energy minimization was done with the steepest descent algorithm in 5,000 steps. The non-hydrogen atoms of the ligands were restrained, and system equilibration was done in two steps including NVT and NPT ensembles in 10 ns at 300 K in atmospheric condition (1 atm). Finally, production MD was performed 100 ns at 300 K with a 2-femtosecond (fs) time step using Leapfrog integrator. The resultant trajectory was explored to understand the structural dynamics of the complex system through various utility toolkits of GROMACS. Stability parameters including backbone root mean square deviation (RMSD), the radius of gyration (Rg), Cα-root mean squared fluctuations (RMSF), and intermolecular hydrogen bond (H-bond) distributions were computed for the complex system. 2D graphs were plotted using XMGrace, while, interaction images were plotted using BIVIA DSV and PyMOL."}

{"project":"LitCovid-sentences","denotations":[{"id":"T92","span":{"begin":0,"end":216},"obj":"Sentence"},{"id":"T93","span":{"begin":217,"end":331},"obj":"Sentence"},{"id":"T94","span":{"begin":332,"end":465},"obj":"Sentence"},{"id":"T95","span":{"begin":466,"end":535},"obj":"Sentence"},{"id":"T96","span":{"begin":536,"end":623},"obj":"Sentence"},{"id":"T97","span":{"begin":624,"end":752},"obj":"Sentence"},{"id":"T98","span":{"begin":753,"end":938},"obj":"Sentence"},{"id":"T99","span":{"begin":939,"end":1054},"obj":"Sentence"},{"id":"T100","span":{"begin":1055,"end":1197},"obj":"Sentence"},{"id":"T101","span":{"begin":1198,"end":1437},"obj":"Sentence"},{"id":"T102","span":{"begin":1438,"end":1541},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"To study the dynamic behavior, stability, and conformational flexibility RBD-ACE2- naltrexone complex, all-atoms MD simulations were performed as reported previously (Dehury et al., 2014; 2017; Girdhar et al., 2019). CHARMM36 force fields were used for topology building of protein in GROMACSv2019.4 package (Abraham et al., 2015). The ligand topology was derived from CHARMM General Force Field (https://cgenff.umaryland.edu/) (Vanommeslaeghe and MacKerell, 2012). The structure was solvated in a cubic water box in TIP3P water model. The system charge was electro-neutralized by adding 0.15 M NaCl to the solvated system. To eliminate bad contacts in the complex system energy minimization was done with the steepest descent algorithm in 5,000 steps. The non-hydrogen atoms of the ligands were restrained, and system equilibration was done in two steps including NVT and NPT ensembles in 10 ns at 300 K in atmospheric condition (1 atm). Finally, production MD was performed 100 ns at 300 K with a 2-femtosecond (fs) time step using Leapfrog integrator. The resultant trajectory was explored to understand the structural dynamics of the complex system through various utility toolkits of GROMACS. Stability parameters including backbone root mean square deviation (RMSD), the radius of gyration (Rg), Cα-root mean squared fluctuations (RMSF), and intermolecular hydrogen bond (H-bond) distributions were computed for the complex system. 2D graphs were plotted using XMGrace, while, interaction images were plotted using BIVIA DSV and PyMOL."}

{"project":"2_test","denotations":[{"id":"32930058-24847713-56195693","span":{"begin":182,"end":186},"obj":"24847713"},{"id":"32930058-27923179-56195694","span":{"begin":188,"end":192},"obj":"27923179"},{"id":"32930058-30296922-56195695","span":{"begin":210,"end":214},"obj":"30296922"},{"id":"32930058-23146088-56195696","span":{"begin":459,"end":463},"obj":"23146088"}],"text":"To study the dynamic behavior, stability, and conformational flexibility RBD-ACE2- naltrexone complex, all-atoms MD simulations were performed as reported previously (Dehury et al., 2014; 2017; Girdhar et al., 2019). CHARMM36 force fields were used for topology building of protein in GROMACSv2019.4 package (Abraham et al., 2015). The ligand topology was derived from CHARMM General Force Field (https://cgenff.umaryland.edu/) (Vanommeslaeghe and MacKerell, 2012). The structure was solvated in a cubic water box in TIP3P water model. The system charge was electro-neutralized by adding 0.15 M NaCl to the solvated system. To eliminate bad contacts in the complex system energy minimization was done with the steepest descent algorithm in 5,000 steps. The non-hydrogen atoms of the ligands were restrained, and system equilibration was done in two steps including NVT and NPT ensembles in 10 ns at 300 K in atmospheric condition (1 atm). Finally, production MD was performed 100 ns at 300 K with a 2-femtosecond (fs) time step using Leapfrog integrator. The resultant trajectory was explored to understand the structural dynamics of the complex system through various utility toolkits of GROMACS. Stability parameters including backbone root mean square deviation (RMSD), the radius of gyration (Rg), Cα-root mean squared fluctuations (RMSF), and intermolecular hydrogen bond (H-bond) distributions were computed for the complex system. 2D graphs were plotted using XMGrace, while, interaction images were plotted using BIVIA DSV and PyMOL."}