Protein Structure and Function: Application of Bioinformatics Methods - John Rigden 2014

Protein Dynamics: From Structure to Function
Methods for Predicting Functional Modes
Elastic Network Models

Elastic or Gaussian network models (ENMs) (Tirion 1996) are, essentially, a simplified approach to Structure/143.html">Normal Mode Analysis. Typically, instead of a full-atom protein representation, only its Ca atoms are taken into account. This results in a tenfold reduction in the number of particles, which dramatically decreases computational costs. Furthermore, since the initial coordinates are assumed to correspond to the ground state, energy Minimization is not required.

The potential energy is calculated According to the formula

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where y denotes the stiffness constant, and RC stands for the cut-off radius. Compared to the strong assumptions inherent in normal mode analysis, such simplifications do not lead to a significant loss of quality. This circumstance, along with the relatively low computational cost, explains the current popularity of such elastic network models. ENM algorithm implementations are also available on web servers such as ElNemo (Suhre and Sanejouand 2004a, b) (http://www.igs.cnrs-mrs.fr/elnemo/) and AD-ENM (Zheng and Doniach 2003; Zheng and Brooks 2005) (http://enm.lobos.nih.gov/).



Last update: 06/08/2026

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