Visual cavity analysis in molecular simulations
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.
J. Parulek, C. Turkay, N. Reuter, and I. Viola, "Visual cavity analysis in molecular simulations," BMC Bioinformatics, vol. 14, iss. Suppl 19, p. S4, 2013. doi:10.1186/1471-2105-14-S19-S4
[BibTeX]
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.
@ARTICLE {Parulek13Visual,
author = "Julius Parulek and Cagatay Turkay and Nathalie Reuter and Ivan Viola",
title = "Visual cavity analysis in molecular simulations",
journal = "BMC Bioinformatics",
year = "2013",
volume = "14",
number = "Suppl 19",
pages = "S4",
month = "Nov.",
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.",
images = "images/Parulek13Visual01.png, images/Parulek13Visual02.png",
thumbnails = "images/Parulek13Visual01_thumb.png, images/Parulek13Visual02_thumb.png",
url = "//www.biomedcentral.com/1471-2105/14/S19/S4",
doi = "10.1186/1471-2105-14-S19-S4",
issn = "1471-2105",
project = "physioillustration"
}