Visual Cavity Analysis in Molecular Simulations
Peer reviewed, Journal article
Peer reviewed
Permanent lenke
https://hdl.handle.net/1956/8305Utgivelsesdato
2013-11-12Metadata
Vis full innførselSamlinger
Originalversjon
https://doi.org/10.1186/1471-2105-14-s19-s4Sammendrag
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.
Utgiver
BioMed CentralTidsskrift
BMC BioinformaticsOpphavsrett
Julius Parulek et al.; licensee BioMed Central Ltd.Copyright 2013 Parulek et al; licensee BioMed Central Ltd.