Anisotropic network model: systematic evaluation and a new web interface.
BACKGROUND
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.


BACKGROUND
ANM server (http://www.ccbb.pitt.edu/anm)
Eyal
Eran
E
Department of Computational Biology, School of Medicine, University of Pittsburgh, PA 15213, USA.
Yang
Lee-Wei
LW
Bahar
Ivet
I
D000465:Algorithms; D016880:Anisotropy; D003198:Computer Simulation; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D012986:Software Validation; D014584:User-Computer Interface
D011506:Proteins