Paper Citing NAMD - Abstract
Romo, Tod D.; Grossfield, Alan
Validating and improving elastic network models with molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 79:23-34, JAN 2011
Elastic network models (ENMs) are a class of simple models intended to represent the collective motions of proteins. In contrast to all-atom molecular dynamics simulations, the low computational investment required to use an ENM makes them ideal for speculative hypothesis-testing situations. Historically, ENMs have been validated via comparison to crystallographic B-factors, but this comparison is relatively low-resolution and only tests the predictions of relative flexibility. In this work, we systematically validate and optimize a number of ENM-type models by quantitatively comparing their predictions to microsecond-scale all-atom simulations of three different G protein coupled receptors. We show that, despite their apparent simplicity, well-optimized ENMs perform remarkably well, reproducing the protein fluctuations with an accuracy comparable to what one would expect from all-atom simulations run for several hundred nanoseconds. Proteins 2011; 79: 23-34. (C) 2010 Wiley-Liss, Inc.
