Reply to 'Comment on elastic network models and proteins'

Abstract

The Gaussian network model (GNM) is based on the underlying assumption of isotropic and Gaussian fluctuations of residues controlled by inter-residue contact topology, similar to the statistical theory of junction fluctuations developed by Flory and coworkers for polymer networks. We clarify here these underlying assumptions and emphasize the fact that the GNM predictions (e.g. mean-square fluctuations, cross-correlations and global mode shapes) are rotationally invariant and more accurate than their counterparts predicted by elastic network normal mode analysis.