oGNM: online computation of structural dynamics using the Gaussian Network Model

An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperativefluctuationsaccessibleundernativestate conditions, is a first step towards understanding molecular mechanisms relevant to biological function. We present a web-based system, oGNM that enables users to calculate online the shape and dispersion of normal modes of motion for proteins, oligonucleotides and their complexes, or associated biological units, using the Gaussian Network Model (GNM). Computations with the new engine are 5

• Type: Journal
• Year: 2006
• Where: NAR
• Authors: Lee-Wei Yang, A. J. Rader, Xiong Liu, Christopher Jon Jursa, Shann-Ching Chen, Hassan A. Karimi, Ivet Bahar
• Keywords: Gaussian Network Model, NAR 2006, Normal Mode, Normal Mode Analyses