New publication: ENCoM - Normal modes to simulate protein dynamics and its applications By: matthieu chartier May 16 2014
Our manuscript: A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations is now available on the PLOS Computational Biology website.
In this paper we describe a new Normal Mode Analysis (NMA) model that takes into account the primary structure of protein. This new inclusion have improved significantly the conformational change predictions on loop and domain movements compared to one of the most used NMA model:Anisotropic Network Model. Moreover, we used the predicted movements to estimate a conformational entropic term to a given protein structure. A look at single point mutation effect on protein stability have shown that ENCoM's predictions correlate well with experimental data. ENCoM performance is similar when tested on most models of the whole dataset, but significantly better to predict mutations that stabilize the protein. Also, ENCoM has been shown to be a more self-consistent model, being least sensitive to the initial structure.