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PMC:7544934 / 11171-12712 JSONTXT

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LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
271 77-81 Gene denotes ACE2 Gene:59272
272 933-936 Gene denotes atm Gene:472
273 504-509 Chemical denotes water MESH:D014867
274 523-528 Chemical denotes water MESH:D014867
275 595-599 Chemical denotes NaCl MESH:D012965
276 761-769 Chemical denotes hydrogen MESH:D006859
277 1363-1371 Chemical denotes hydrogen MESH:D006859
278 107-115 Disease denotes atoms MD MESH:D009436
279 369-375 Disease denotes CHARMM

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T92 0-216 Sentence denotes 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).
T93 217-331 Sentence denotes CHARMM36 force fields were used for topology building of protein in GROMACSv2019.4 package (Abraham et al., 2015).
T94 332-465 Sentence denotes The ligand topology was derived from CHARMM General Force Field (https://cgenff.umaryland.edu/) (Vanommeslaeghe and MacKerell, 2012).
T95 466-535 Sentence denotes The structure was solvated in a cubic water box in TIP3P water model.
T96 536-623 Sentence denotes The system charge was electro-neutralized by adding 0.15 M NaCl to the solvated system.
T97 624-752 Sentence denotes To eliminate bad contacts in the complex system energy minimization was done with the steepest descent algorithm in 5,000 steps.
T98 753-938 Sentence denotes 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).
T99 939-1054 Sentence denotes Finally, production MD was performed 100 ns at 300 K with a 2-femtosecond (fs) time step using Leapfrog integrator.
T100 1055-1197 Sentence denotes The resultant trajectory was explored to understand the structural dynamics of the complex system through various utility toolkits of GROMACS.
T101 1198-1437 Sentence denotes 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.
T102 1438-1541 Sentence denotes 2D graphs were plotted using XMGrace, while, interaction images were plotted using BIVIA DSV and PyMOL.

2_test

Id Subject Object Predicate Lexical cue
32930058-24847713-56195693 182-186 24847713 denotes 2014
32930058-27923179-56195694 188-192 27923179 denotes 2017
32930058-30296922-56195695 210-214 30296922 denotes 2019
32930058-23146088-56195696 459-463 23146088 denotes 2012