Visual cavity analysis in molecular simulations

BMC Bioinformatics

Research

Nathalie Reuter¹  Julius Parulek²  Cagatay Turkay²  Ivan Viola³ 

[1] CBU, University of Bergen, Norway;Department of Informatics, University of Bergen, Norway;Department of Informatics, University of Bergen, Norway;Vienna University of Technology, Austria;

关键词: Molecular Dynamic Simulation;    Voronoi Diagram;    Molecular Surface;    Implicit Surface;    Amino Acid Type;   

DOI  :  10.1186/1471-2105-14-S19-S4

来源: Springer

【 摘 要 】

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.

【 授权许可】

CC BY   
© Parulek et al; licensee BioMed Central Ltd. 2013