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Implicit surfaces for interactive graph based cavity analysis of molecular simulations

Parulek, J., Turkay, C., Reuter, N. & Viola, I. (2012). Implicit surfaces for interactive graph based cavity analysis of molecular simulations. In: IEEE Symposium on Biological Data Visualization 2012, BioVis 2012 - Proceedings. 2nd IEEE Symposium on Biological Data Visualization, 14 Dec - 15 Dec 2012, Seattle, USA.


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 context 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 context 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.

Publication Type: Conference or Workshop Item (Paper)
Additional Information: © 2012 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Publisher Keywords: Computer Applications, Life and Medical Sciences—Biology and Genetics, Computer Graphics, Computational Geometry and Object Modeling—Boundary representations, Curve, surface, solid, object representations
Subjects: T Technology > TA Engineering (General). Civil engineering (General)
Departments: School of Science & Technology > Computer Science
School of Science & Technology > Computer Science > giCentre
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