Sentence examples for molecular dynamics refinement from inspiring English sources

The model obtained from MOE was refined using the molecular dynamics refinement tool YASARA and stereochemical quality was analyzed with PROCHECK [32].

After the molecular dynamics refinement, the optimized homology model was assessed as a reliable structure by PROCHECK, ERRAT, WHAT-IF, PROSA2003 and DOPE graph.

The structure of Plasmodium vivax dihydrofolate reductase (PvDHFR), a potentially important target for antimalarial chemotherapy, was determined by means of homology modeling and molecular dynamics refinement.

Following molecular dynamics refinement, side-chain interactions at the protein interface were identified that were predicted to contribute substantially to the free energy of binding.

In this study, we applied ligand docking and molecular dynamics refinement to a P2Y14R homology model to qualitatively explain structure activity relationships of previously published synthetic nucleotide analogues and to probe the quality of P2Y14R homology modeling as a template for structure-based design.

The coarse-grained structures serve as the initial structures for all-atom molecular dynamics refinement to build the final all-atom 3D structures.

For further model refinement the top scoring model was submitted to the FG-MD server for fragment guided molecular dynamics structure refinement [ 74].

In addition, docking and Molecular dynamics (MD) refinement of the B7-Hsp90 complex showed that the binding model of B7 to Hsp90 was similar with that of 8-benzyladenines.

In order to address these issues, we constructed structural models of lurasidone GPCR complexes by homology modeling of receptors, exhaustive docking of ligand, and molecular dynamics simulation-based refinement of complexes.

Modeller9v2's [ 37] script for automated model generation using homology modeling was run with successive molecular dynamics simulated for annealing refinement (refine.slow).slow

The new program OPAL for molecular dynamics simulations and energy refinements of biological macromolecules.