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Briefings in Bioinformatics Advance Access originally published online on May 7, 2007
Briefings in Bioinformatics 2007 8(6):432-445; doi:10.1093/bib/bbm014
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© The Author 2007. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

High-throughput modeling and analysis of protein structural dynamics

Xiong Liu and Hassan A. Karimi

Corresponding author. Xiong Liu, Wilmer Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. Tel: +1-410-502-2955; Fax: +1-410-502-5382; E-mail: xliu33{at}jhmi.edu

Protein function is a dynamic property closely related to the conformational mechanisms of protein structure in its physiological environment. To understand and control the function of target proteins, it becomes increasingly important to develop methods and tools for predicting collective motions at the molecular level. In this article, we review computational methods for predicting conformational dynamics and discuss software tools for data analysis. In particular, we discuss a high-throughput, web-based system called iGNM for protein structural dynamics. iGNM contains a database of protein motions for more than 20 000 PDB structures and supports online calculations for newly deposited PDB structures or user-modified structures. iGNM allows dynamics analysis of protein structures ranging from enzymes to large complexes and assemblies, and enables the exploration of protein sequence–structure–dynamics–function relations.

Keywords: protein dynamics, protein function, normal mode analysis, elastic network models, databases, web-based systems

Submitted: October 12, 2006.
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