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Bioinformatics Advance Access published online on August 23, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl448
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© 2006 The Author(s)
Received June 2, 2006
Revised August 1, 2006
Accepted August 16, 2006

Article

Anisotropic Network Model: systematic evaluation and a new web interface

Eran Eyal 1 *, Lee-Wei Yang 1, and Ivet Bahar 1

1 Department of Computational Biology, School of Medicine, University of Pittsburgh, PA 15213, USA

* To whom correspondence should be addressed.
Eran Eyal, E-mail: eyal{at}ccbb.pitt.edu


  Abstract

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 non-globular 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.

Associate Editor: Anna Tramontano
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