This motivated efforts for developing efficient, but physically realistic, methods for deriving dynamic properties based on structure. Time cost of molecular dynamics simulations has been a major drawback for a systematic computational characterization of protein dynamics.
It is now widely recognized that efficient computational methods and tools are needed for understanding the dynamics, and thereby controlling the function of proteins and their complexes. It is closely related to conformational mechanics which, in turn, is largely dictated by the equilibrium (native) structure. A case study of the dynamics of 20 non-homologous hydrolases is presented to illustrate the utility of the iGNM database for identifying key residues that control the cooperative motions and revealing the connection between collective dynamics and catalytic activity.Ĭontact: and the rapid accumulation of protein structures in the Protein Data Bank (PDB) ( Berman et al., 2000) it has become evident that structural information per se is not sufficient for gaining insights into the mechanisms of function. Static and animated images for describing the conformational mobility of proteins over a broad range of normal modes are accessible, along with an online calculation engine available for newly deposited structures.
#Gaussian software pop download#
The results are stored on a web-based system called iGNM and configured so as to permit the users to visualize or download the results through a standard web browser using a simple search engine. Results: We computed the GNM dynamics for 20 058 structures from the Protein Data Bank, and generated information on the equilibrium dynamics at the level of individual residues.
The recent success of analytical methods based on elastic network models, and in particular the Gaussian Network Model (GNM), permits us to perform a high-throughput analysis of the collective dynamics of proteins. Although protein structural information has been rapidly accumulating in databases, little effort has been invested to date toward systematically characterizing protein dynamics. Motivation: The knowledge of protein structure is not sufficient for understanding and controlling its function.
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