Implicit Surfaces for Interactive Graph Based Cavity Analysis of Molecular Simulations

Julius Parulek, Cagatay Turkay, Natalie Reuter, Ivan Viola

INPROCEEDINGS, 2nd IEEE Symposium on Biological Data Visualization, 2012

• paper

Abstract

Molecular surfaces provide a suitable way to analyze and to study the evolution and interaction of molecules. The analysis is often concerned with visual identification of binding sites of ligands to a host macromolecule. We present a novel technique that is based on implicit representation, which extracts all potential binding sites and allows an advanced 3D visualization of these sites in the con- text of the molecule. We utilize implicit function sampling strategy to obtain potential cavity samples and graph algorithms to extract arbitrary cavity components defined by simple graphs. Moreover, we propose how to interactively visualize these graphs in the con- text of the molecular surface. We also introduce a system of linked views depicting various graph parameters that are used to perform a more elaborative study on created graphs.

Published

2nd IEEE Symposium on Biological Data Visualization

• Series: BioVis 2012
• Location: Seattle (WA), US

Media

BibTeX

@inproceedings{Parulek12Implicit,
 author = {Julius Parulek and Cagatay Turkay and Natalie Reuter and Ivan Viola},
 title = {Implicit Surfaces for Interactive Graph Based Cavity Analysis
   of Molecular Simulations},
 booktitle={2nd IEEE Symposium on Biological Data Visualization},
 series = {BioVis 2012},
 year = {2012},
 location = {Seattle (WA), US},
 abstract = {Molecular surfaces provide a suitable way to analyze and to study
   the evolution and interaction of molecules. The analysis is often
   concerned with visual identification of binding sites of ligands to
   a host macromolecule. We present a novel technique that is based
   on implicit representation, which extracts all potential binding sites
   and allows an advanced 3D visualization of these sites in the con-
   text of the molecule. We utilize implicit function sampling strategy
   to obtain potential cavity samples and graph algorithms to extract
   arbitrary cavity components defined by simple graphs. Moreover,
   we propose how to interactively visualize these graphs in the con-
   text of the molecular surface. We also introduce a system of linked
   views depicting various graph parameters that are used to perform
   a more elaborative study on created graphs.},



}