WEBnm@: a web application for normal mode analyses of proteins

We developed a web-based server to perform normal modes calculations and different types of analyses. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations; normalized squared atomic displacements, vector field representation and animation of the first six vibrational modes. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to analyze the results with their favorite software, raw results can also be downloaded. The application is available on http://www.bioinfo.no/tools/normalmodes webcite. We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example.We built an efficient and modular web application for normal mode analysis of proteins. Non specialists can easily and rapidly evaluate the degree of flexibility of multi-domain protein assemblies and characterize the large amplitude movements of their domains.Molecular modeling provides several powerful tools for computing the dynamics of proteins. Normal Mode Analysis (NMA) is a well suited approach to study dynamics of proteins, especially when the protein is relatively big (several thousand amino acids) and the time scale of the dynamical events of interest are longer than what molecular dynamics (MD) simulations can reach, typically a few nanoseconds. These methods are based on the hypothesis that the vibrational normal modes exhibiting the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones functionally relevant.Several tools based on NMA have been developed [1-16] and successfully applied to predict the collective, large amplitude motions of several macromolecules of different sizes, e.g. the F(1)-APTase[17], RNA pol