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

Abstract

Background: Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or vi rus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest fr equencies (also named soft modes) describe the largest movements in a protein and are th e ones that are functionally relevant. Results: We developed a web-based server to perfor m 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 offe rs the user a series of automated calculations; normalized squared atomic displace ments, 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 wi th their favorite software, raw results can also be downloaded. The application is available on http://www.bioinfo.no/tools/normalmodes . We present here the underlying theory, the application architecture an d an illustration of its features using a large transmembrane protein as an example. Conclusion: We built an efficient and modular web a pplication for normal mode analysis of proteins. Non specialists can easily and rapidly ev aluate the degree of flex ibility of multi-domain protein assemblies and characterize the la rge amplitude movements of their domains.