LitCovid-sentences  

PMC:7081066 / 3629-5135 JSONTXT 13 Projects

Annnotations TAB TSV DIC JSON TextAE

Id Subject Object Predicate Lexical cue
T31 0-241 Sentence denotes Homology structural models of viral spike protein from SARS-CoV-2 (QHO62112.1) and Bat-CoV (AAZ67052.1) were built by using the tools of the SWISS-MODEL modeling server and the DeepView/Swiss-PdbViewer 4.01 software (Arnold et al., 2006[1]).
T32 242-319 Sentence denotes Several models were obtained and the quality of each structure was evaluated.
T33 320-439 Sentence denotes The best model for SARS-CoV-2 spike was obtained using the crystal structure of SARS-CoV spike protein (PDB code 6ACC).
T34 440-554 Sentence denotes On the other hand, for Bat-CoV, the best model was obtained using as template the crystal structure PDB code 6ACD.
T35 555-625 Sentence denotes These models were subjected to further protein structure optimization.
T36 626-712 Sentence denotes Hydrogen atoms were added and the partial charges were assigned for energy refinement.
T37 713-765 Sentence denotes The protein model was embedded in a 100 Å water box.
T38 766-956 Sentence denotes Then, energy minimization was performed while applying constraints to the protein backbone to preserve global folding and optimizing the relative position of the water molecules and protein.
T39 957-1054 Sentence denotes The obtained systems underwent MD simulations using NAMD as described by Ortega et al. (2019[8]).
T40 1055-1201 Sentence denotes All MD simulations described in this study were performed with NAMD 2.12 (Phillips et al., 2005[10]), Vega ZZ 3.1.0.21 (Pedretti et al., 2004[9]).
T41 1202-1287 Sentence denotes CHARMM force field (Vanommeslaeghe et al., 2010[14]) and Gasteiger charges were used.
T42 1288-1368 Sentence denotes The obtained structures represent the lowest energy frame of the MD simulations.
T43 1369-1506 Sentence denotes The quality of the models was established with ProSA (Wiederstein and Sippl, 2007[17]) and PROCHECK programs (Laskowski et al., 1993[4]).