WEBnm@: a web application for normal mode analyses of proteins.
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 virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant.


RESULTS
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. We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example.


CONCLUSIONS
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.
Hollup
Siv Midtun
SM
Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Thormøhlensgt. 55, N-5008 Bergen, Norway. sivh@ii.uib.no
Salensminde
Gisle
G
Reuter
Nathalie
N
D000465:Algorithms; D000252:Calcium-Transporting ATPases / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D003593:Cytoplasm / Q000378:metabolism; D003628:Database Management Systems; D030562:Databases, Protein; D005822:Genetic Vectors; D016247:Information Storage and Retrieval; D020407:Internet; D015233:Models, Statistical; D015394:Molecular Structure; D009696:Nucleic Acids; D010455:Peptides; D011487:Protein Conformation; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface
D009696:Nucleic Acids; D010455:Peptides; D011506:Proteins; D053498:Sarcoplasmic Reticulum Calcium-Transporting ATPases; D000252:Calcium-Transporting ATPases