نتایج جستجو برای: charmm

تعداد نتایج: 456  

2002
M. Taufer T. Stricker G. Settanni A. Cavalli

CHARMM is a popular molecular dynamics code for computational biology. For many CHARMM applications such as protein folding, desktop grids could become viable alternatives to clusters of PCs. In this technical report, we present a prototype and discuss the viability of a protein folding application with CHARMM on the United Devices MetaProcessor, a platform for widely distributed computing. We ...

2003
Bennet Uk Michela Taufer Thomas Stricker Giovanni Settanni Andrea Cavalli

CHARMM is a popular molecular dynamics code for computational biology. For many CHARMM applications such as protein folding, desktop grids could become viable alternatives to clusters of PCs. In this paper, we present a prototype and discuss the viability of a protein folding application with CHARMM on the United Devices MetaProcessor, a platform for widely distributed computing. We identify th...

Journal: :Structure 2007
Dmitry A Kondrashov Adam W Van Wynsberghe Ryan M Bannen Qiang Cui George N Phillips

Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. We use anisotropic displacement parameters from crystallography to test the quality of prediction of both the magnitude and directionality of conformational flexibility. Normal modes from four simple elastic network model potentials and from the CHARMM force field are calculated for a ...

Journal: :Biophysical Journal 2015

Journal: :Journal of Computational Chemistry 2009

Journal: :Journal of computational chemistry 2004
Michael Patra Mikko Karttunen

In this article we compare different force fields that are widely used (Gromacs, Charmm-22/x-Plor, Charmm-27, Amber-1999, OPLS-AA) in biophysical simulations containing aqueous NaCl. We show that the uncertainties of the microscopic parameters of, in particular, sodium, and, to a lesser extent, chloride, translate into large differences in the computed radial-distribution functions. This uncert...

Journal: :Journal of medicinal chemistry 2004
Philippe Ferrara Holger Gohlke Daniel J Price Gerhard Klebe Charles L Brooks

An assessment of nine scoring functions commonly applied in docking using a set of 189 protein-ligand complexes is presented. The scoring functions include the CHARMm potential, the scoring function DrugScore, the scoring function used in AutoDock, the three scoring functions implemented in DOCK, as well as three scoring functions implemented in the CScore module in SYBYL (PMF, Gold, ChemScore)...

A. R. Illchani F. Kaveh K. zare N. Khodayari S. Salemi

This paper investigates the mechanism of water transportation through aquaporin-4(AQP4) of ratbrain cells by means of molecular dynamics simulation with CHARMM software. The AQP4 wasembedded into a bilayer made of Dimystroilphosphatylcholine (DMPC). The results illustrate thatwater molecules move through AQP4's channel with change of orientation of oxygen of eachwater molecule.

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