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Visual cavity analysis in molecular simulations

Julius Parulek, Cagatay Turkay, Nathalie Reuter, Ivan Viola

ARTICLE, BMC Bioinformatics, Nov., 2013

Abstract

Molecular surfaces provide a useful mean for analyzing interactions between biomolecules; such as identification and characterization of ligand binding sites to a host macromolecule. We present a novel technique, which extracts potential binding sites, represented by cavities, and characterize them by 3D graphs and by amino acids. The binding sites are extracted using an implicit function sampling and graph algorithms. We propose an advanced cavity exploration technique based on the graph parameters and associated amino acids. Additionally, we interactively visualize the graphs in the context of the molecular surface. We apply our method to the analysis of MD simulations of Proteinase 3, where we verify the previously described cavities and suggest a new potential cavity to be studied.

Published

BMC Bioinformatics

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BibTeX

@ARTICLE{Parulek13Visual, 
 author={Julius Parulek and Cagatay Turkay and Nathalie Reuter and Ivan Viola}, 
 journal={BMC Bioinformatics}, 
 title={Visual cavity analysis in molecular simulations}, 
 volume = {14},
 number = {Suppl 19},
 pages = {S4},
 url = {http://www.biomedcentral.com/1471-2105/14/S19/S4},
 doi = {10.1186/1471-2105-14-S19-S4},
 issn = {1471-2105},
 month = {Nov.},
 year={2013},
 abstract = {Molecular surfaces provide a useful mean for analyzing interactions 
 between biomolecules; such as identification and characterization of ligand 
 binding sites to a host macromolecule. We present a novel technique, which extracts 
 potential binding sites, represented by cavities, and characterize 
 them by 3D graphs and by amino acids. The binding sites are extracted using an 
 implicit function sampling and graph algorithms. We propose an advanced cavity 
 exploration technique based on the graph parameters and associated amino acids. 
 Additionally, we interactively visualize the graphs in the context of the 
 molecular surface. We apply our method to the analysis of MD simulations of 
 Proteinase 3, where we verify the previously described cavities and suggest a 
 new potential cavity to be studied.},

}






 Last Modified: Jean-Paul Balabanian, 2014-02-28