Sentence examples for molecular dynamics tools from inspiring English sources

In contrast to the gold standard of long-term storage experiments applied in industry, novel experimental and in silico molecular dynamics tools for predicting protein solution stability can be applied within several minutes or hours.

39,  40,  41 Clash regions in resulting dimers were refined with the molecular dynamics tools of SYBYL-X by using the Amber7 forcefield field 43.

The new supercomputer is distinguished from other molecular dynamics computing tools like I.B.M.'s BlueGene/L supercomputer and the Stanford Folding@home distributed computing project in that the machine is designed to simulate a very narrow set of problems on biological processes that take place over a millisecond or longer.

Discrete models underpin state-of-the-art molecular dynamics simulation tools.

In this in silico study, a previously developed molecular dynamics (MD) tool is used, which simulates any given biomolecule on resins with varying ligand densities.

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

Geometry was optimized using simulated annealing algorithm with the help of Desmond molecular dynamics simulations software tool.

Secondly, quite recently a freeware molecular dynamics trajectory analysis tool has been released 9 that is fully compatible with Gromacs.

In this study, the effect of alcohols as solvents on the kinetics and the tacticity of poly N-Isopropylacrylamide) (poly N-Isopropylacrylamideth a combined static and molecular dynamics set of comPNIPAMonal tools.

The potential of mean force simulations, widely applied in Monte Carlo or molecular dynamics simulations, are useful tools to examine the free energy variation as a function of one or more specific reaction coordinate(s) for a given system.

Molecular dynamics simulations are excellent tools for identifying such sites [ 39- 41].