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 ...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Siv Midtun Hollup, Gisle Sælensminde, Nathalie Reuter
• Keywords: BMCBI 2005, Normal Mode, Normal Mode Analysis, Protein