Bioinformatics Advance Access originally published online on August 23, 2006
Bioinformatics 2006 22(21):2619-2627; doi:10.1093/bioinformatics/btl448
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© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Anisotropic network model: systematic evaluation and a new web interface
Department of Computational Biology, School of Medicine, University of Pittsburgh PA 15213, USA
*To whom correspondence should be addressed.
Motivation: The Anisotropic Network Model (ANM) is a simple yet powerful model for normal mode analysis of proteins. Despite its broad use for exploring biomolecular collective motions, ANM has not been systematically evaluated to date. A lack of a convenient interface has been an additional obstacle for easy usage.
Results: ANM has been evaluated on a large set of proteins to establish the optimal model parameters that achieve the highest correlation with experimental data and its limits of accuracy and applicability. Residue fluctuations in globular proteins are shown to be more accurately predicted than those in nonglobular proteins, and core residues are more accurately described than solvent-exposed ones. Significant improvement in agreement with experiments is observed with increase in the resolution of the examined structure. A new server for ANM calculations is presented, which offers flexible options for controlling model parameters and output formats, interactive animation of collective modes and advanced graphical features.
Availability: ANM server (http://www.ccbb.pitt.edu/anm)
Contact: bahar{at}ccbb.pitt.edu
Received on June 2, 2006; revised on August 1, 2006; accepted on August 16, 2006
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