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PMC:7441777 / 13861-16786 JSONTXT

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LitCovid-PD-MONDO

Id Subject Object Predicate Lexical cue mondo_id
T49 802-805 Disease denotes BCC http://purl.obolibrary.org/obo/MONDO_0005341
T50 1450-1453 Disease denotes PME http://purl.obolibrary.org/obo/MONDO_0020074

LitCovid-PD-CLO

Id Subject Object Predicate Lexical cue
T92 66-68 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T93 223-224 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T94 360-364 http://purl.obolibrary.org/obo/CLO_0001185 denotes 2018
T95 390-392 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD
T96 751-756 http://purl.obolibrary.org/obo/UBERON_0007688 denotes field
T97 1302-1305 http://purl.obolibrary.org/obo/CLO_0001562 denotes a 2
T98 1302-1305 http://purl.obolibrary.org/obo/CLO_0001563 denotes a 2
T99 1356-1357 http://purl.obolibrary.org/obo/CLO_0001020 denotes Å
T100 1580-1581 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T101 1607-1609 http://purl.obolibrary.org/obo/CLO_0008491 denotes ps
T102 1727-1728 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T103 2027-2028 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T104 2084-2087 http://purl.obolibrary.org/obo/CLO_0001562 denotes Å−2
T105 2084-2087 http://purl.obolibrary.org/obo/CLO_0001563 denotes Å−2
T106 2402-2403 http://purl.obolibrary.org/obo/CLO_0001020 denotes a
T107 2435-2439 http://purl.obolibrary.org/obo/CLO_0001146 denotes 1Å−2
T108 2495-2497 http://purl.obolibrary.org/obo/CLO_0007622 denotes MD

LitCovid-PD-CHEBI

Id Subject Object Predicate Lexical cue chebi_id
T226 41-45 Chemical denotes atom http://purl.obolibrary.org/obo/CHEBI_33250
T227 66-68 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T228 146-157 Chemical denotes polyphenols http://purl.obolibrary.org/obo/CHEBI_26195
T229 211-221 Chemical denotes remdesivir http://purl.obolibrary.org/obo/CHEBI_145994
T230 241-250 Chemical denotes inhibitor http://purl.obolibrary.org/obo/CHEBI_35222
T231 390-392 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T232 470-473 Chemical denotes RTX http://purl.obolibrary.org/obo/CHEBI_8809
T233 649-658 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T234 798-801 Chemical denotes AM1 http://purl.obolibrary.org/obo/CHEBI_140154
T235 990-995 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T236 1020-1025 Chemical denotes water http://purl.obolibrary.org/obo/CHEBI_15377
T237 1026-1035 Chemical denotes molecules http://purl.obolibrary.org/obo/CHEBI_25367
T238 1159-1161 Chemical denotes Na http://purl.obolibrary.org/obo/CHEBI_26708
T239 1163-1166 Chemical denotes ion http://purl.obolibrary.org/obo/CHEBI_24870
T240 1196-1204 Chemical denotes hydrogen http://purl.obolibrary.org/obo/CHEBI_49637
T241 1205-1210 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T242 1962-1967 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T243 2461-2466 Chemical denotes atoms http://purl.obolibrary.org/obo/CHEBI_33250
T244 2495-2497 Chemical denotes MD http://purl.obolibrary.org/obo/CHEBI_74699
T245 2803-2805 Chemical denotes MM http://purl.obolibrary.org/obo/CHEBI_53458|http://purl.obolibrary.org/obo/CHEBI_74707

LitCovid-PubTator

Id Subject Object Predicate Lexical cue tao:has_database_id
361 236-240 Gene denotes RdRp Gene:43740578
362 614-617 Gene denotes Kar Gene:8083
363 798-801 Species denotes AM1 Tax:408139
364 146-157 Chemical denotes polyphenols MESH:D059808
365 211-221 Chemical denotes remdesivir MESH:C000606551
366 866-877 Chemical denotes antechamber
367 990-995 Chemical denotes water MESH:D014867
368 1020-1025 Chemical denotes water MESH:D014867
369 1196-1204 Chemical denotes hydrogen MESH:D006859
371 2806-2810 Chemical denotes PBSA MESH:C437084

LitCovid-sentences

Id Subject Object Predicate Lexical cue
T149 0-4 Sentence denotes 2.2.
T150 6-36 Sentence denotes Molecular dynamics simulations
T151 37-313 Sentence denotes All-atom molecular dynamics (MD) simulations were performed on the best eight selected plant-derived natural polyphenols obtained from the molecular docking study along with remdesivir, a well-known RdRp inhibitor, for studying thermodynamic stability of the docked structure.
T152 314-359 Sentence denotes The pmemd.cuda module in AMBER18 (Case et al.
T153 360-481 Sentence denotes 2018) was used for conducting MD simulations, and all simulations were performed utilizing the graphics card, RTX 2080Ti.
T154 482-625 Sentence denotes We adopted the same protocol that was used in our earlier studies (Jonniya et al., 2019; Sk, Roy, Jonniya, et al., 2020; Sk, Roy, & Kar, 2020).
T155 626-771 Sentence denotes The receptor and small molecules were described by the Amber ff14SB (Maier et al., 2015) and GAFF2 (Wang et al., 2004) force field, respectively.
T156 772-905 Sentence denotes Ligands were assigned the AM1-BCC (Jakalian et al., 2002) atomic charges calculated using the antechamber (Wang et al., 2001) module.
T157 906-1071 Sentence denotes The complexes were then solvated using an explicit TIP3P (Price & Brooks III, 2004) water model, and nearly 38124 water molecules were needed to solvate each system.
T158 1072-1167 Sentence denotes Subsequently, all solvated systems were neutralized by adding an appropriate number of Na+ ion.
T159 1168-1276 Sentence denotes All bond lengths, including hydrogen atoms, were constrained by the SHAKE algorithm (Kräutler et al., 2001).
T160 1277-1319 Sentence denotes This allows the usage of a 2 fs time-step.
T161 1320-1484 Sentence denotes The non-bonded cut-off was set to 8 Å and the long range electrostatic interactions were evaluated using the particle-mesh Ewald (PME) (Darden et al., 1993) method.
T162 1485-1612 Sentence denotes The temperature was kept at 300 K using the Langevin thermostat (Loncharich et al., 1992) with a collision frequency of 2 ps−1.
T163 1613-1718 Sentence denotes The system pressure was controlled by Berendsen’s Barostat (Berendsen et al., 1984) and fixed at 1.0 bar.
T164 1719-1769 Sentence denotes We used a time-step of 2.0 fs for all simulations.
T165 1770-1814 Sentence denotes Briefly, we used two stages of minimization.
T166 1815-2089 Sentence denotes Firstly, each complex was optimized by 500 steps of steepest descent followed by another 500 steps of conjugate gradient minimization, keeping all atoms of the complex restrained to their initial coordinate with a weak harmonic potential (force constant 2.0 kcal mol−1 Å−2).
T167 2090-2310 Sentence denotes The second stage of minimization was carried out without any restraints by performing 100 steps of steepest descent, followed by another 900 steps of conjugate gradient minimization to remove any residual steric clashes.
T168 2311-2467 Sentence denotes Subsequently, all systems were gradually heated from 0 K to 300 K at the NVT ensemble with a force constant of 2.0 kcal mol−1Å−2 acting on all solute atoms.
T169 2468-2542 Sentence denotes Next, 1.0 ns equilibration MD phase was carried out without any restraint.
T170 2543-2636 Sentence denotes Finally, we performed 150 ns production simulations for all four systems at the NPT ensemble.
T171 2637-2818 Sentence denotes Overall, we accumulated 15000 conformations for each simulation, and we used 500 snapshots from the last 50 ns trajectories for binding affinity estimation using the MM-PBSA scheme.
T172 2819-2925 Sentence denotes The trajectory analysis was done by the AmberTools19 CPPTRAJ (Roe & Cheatham III, 2013) module of Amber18.

2_test

Id Subject Object Predicate Lexical cue
32720577-31656913-56195105 565-569 31656913 denotes 2019
32720577-26574453-56195106 709-713 26574453 denotes 2015
32720577-15116359-56195107 739-743 15116359 denotes 2004
32720577-12395429-56195108 824-828 12395429 denotes 2002
32720577-11457149-56195109 892-896 11457149 denotes 2001
32720577-15549884-56195110 984-988 15549884 denotes 2004
32720577-1515543-56195111 1569-1573 1515543 denotes 1992
32720577-26583988-56195112 2901-2905 26583988 denotes 2013