title: iGNM: a database of protein functional motions based on Gaussian Network Model.
abstract: BACKGROUND
  The knowledge of protein structure is not sufficient for understanding and controlling its function. Function is a dynamic property. Although protein structural information has been rapidly accumulating in databases, little effort has been invested to date toward systematically characterizing protein dynamics. 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.
  
  
  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 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. 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. 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.
authors.affiliation: Department of Computational Biology, School of Medicine, University of Pittsburgh Pittsburgh, PA 15213, USA. lwy1@pitt.edu
authors.forename: Lee-Wei
authors.initials: LW
authors.lastname: Yang
authors.forename: Xiong
authors.initials: X
authors.lastname: Liu
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Jursa
authors.forename: Mark
authors.initials: M
authors.lastname: Holliman
authors.forename: A J
authors.initials: AJ
authors.lastname: Rader
authors.forename: Hassan A
authors.initials: HA
authors.lastname: Karimi
authors.forename: Ivet
authors.initials: I
authors.lastname: Bahar
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D030562:Databases, Protein; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D016011:Normal Distribution; D011485:Protein Binding; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins