Skip Navigation



Bioinformatics Advance Access published online on April 28, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti469
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/13/2978    most recent
bti469v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Yang, L.-W.
Right arrow Articles by Bahar, I.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yang, L.-W.
Right arrow Articles by Bahar, I.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 9, 2005
Revised April 7, 2005
Accepted April 25, 2005

Article

iGNM: a database of protein functional motions based on Gaussian Network Model

Lee-Wei Yang 1*, Xiong Liu 2, Christopher J. Jursa 2, Mark Holliman 1, A. J. Rader 1, Hassan A. Karimi 2, and Ivet Bahar 1

1 Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213
2 Department of Information Science and Telecommunications, University of Pittsburgh, Pittsburgh, PA 15213

* To whom correspondence should be addressed.
Lee-Wei Yang, E-mail: lwy1{at}pitt.edu


  Abstract

Motivation: Knowledge of structure is not sufficient for understanding and controlling protein function. Function is a dynamic property. While protein structural information has been rapidly accumulating in databases, little effort has been invested to date towards systematically characterizing protein dynamics. 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 proteins' collective dynamics.

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 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 twenty 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.

Availability: http://ignm.ccbb.pitt.edu/.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Biophys. JHome page
K. Moritsugu and J. C. Smith
REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes
Biophys. J., August 15, 2008; 95(4): 1639 - 1648.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. David-Eden and Y. Mandel-Gutfreund
Revealing unique properties of the ribosome using a network based analysis
Nucleic Acids Res., August 1, 2008; 36(14): 4641 - 4652.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
J. G. Su, C. H. Li, R. Hao, W. Z. Chen, and C. Xin Wang
Protein Unfolding Behavior Studied by Elastic Network Model
Biophys. J., June 15, 2008; 94(12): 4586 - 4596.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
I. Bartova, J. Koca, and M. Otyepka
Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation
Protein Sci., January 1, 2008; 17(1): 22 - 33.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
K. Moritsugu and J. C. Smith
Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
Biophys. J., November 15, 2007; 93(10): 3460 - 3469.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B. W. Zhang, D. Jasnow, and D. M. Zuckerman
Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
PNAS, November 13, 2007; 104(46): 18043 - 18048.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
X. Liu and H. A. Karimi
High-throughput modeling and analysis of protein structural dynamics
Brief Bioinform, November 1, 2007; 8(6): 432 - 445.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
A. Szarecka, Y. Xu, and P. Tang
Dynamics of Firefly Luciferase Inhibition by General Anesthetics: Gaussian and Anisotropic Network Analyses
Biophys. J., September 15, 2007; 93(6): 1895 - 1905.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
P. M. Jones and A. M. George
Nucleotide-dependent Allostery within the ABC Transporter ATP-binding Cassette: A COMPUTATIONAL STUDY OF THE MJ0796 DIMER
J. Biol. Chem., August 3, 2007; 282(31): 22793 - 22803.
[Abstract] [Full Text] [PDF]

Home page
 Protein Eng Des SelHome page
A. Pandini, G. Mauri, A. Bordogna, and L. Bonati
Detecting similarities among distant homologous proteins by comparison of domain flexibilities
Protein Eng. Des. Sel., June 30, 2007; (2007) gzm021v2.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. I. Garzon, J. Kovacs, R. Abagyan, and P. Chacon
DFprot: a webtool for predicting local chain deformability
Bioinformatics, April 1, 2007; 23(7): 901 - 902.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
E. Eyal, L.-W. Yang, and I. Bahar
Anisotropic network model: systematic evaluation and a new web interface
Bioinformatics, November 1, 2006; 22(21): 2619 - 2627.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L.-W. Yang, A. J. Rader, X. Liu, C. J. Jursa, S. C. Chen, H. A. Karimi, and I. Bahar
oGNM: online computation of structural dynamics using the Gaussian Network Model.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W24 - W31.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Lindahl, C. Azuara, P. Koehl, and M. Delarue
NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W52 - W56.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Jang, J. I. Jeong, and M. K. Kim
UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W57 - W62.
[Abstract] [Full Text] [PDF]

Home page
 Biophys. JHome page
P. Petrone and V. S. Pande
Can Conformational Change Be Described by Only a Few Normal Modes?
Biophys. J., March 1, 2006; 90(5): 1583 - 1593.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.