Extraction of Robust Voids and Pockets in Proteins

Abstract
Voids and pockets in a protein refer to empty spaces that are enclosed by the protein molecule. Existing methods to compute, measure, and visualize the voids and pockets in a protein molecule are sensitive to inaccuracies in the empirically determined atomic radii. This paper presents a topological framework that enables robust computation and visualization of these structures. Given a fixed set of atoms, voids and pockets are represented as subsets of the weighted Delaunay triangulation of atom centers. A novel notion of (e;p)-stable voids helps identify voids that are stable even after perturbing the atom radii by a small value. An efficient method is described to compute these stable voids for a given input pair of values (e;p).
Description

        
@inproceedings{
:10.2312/PE.EuroVisShort.EuroVisShort2013.067-071
, booktitle = {
EuroVis - Short Papers
}, editor = {
Mario Hlawitschka and Tino Weinkauf
}, title = {{
Extraction of Robust Voids and Pockets in Proteins
}}, author = {
Sridharamurthy, Raghavendra
and
Doraiswamy, Harish
and
Patel, Siddharth
and
Varadarajan, Raghavan
and
Natarajan, Vijay
}, year = {
2013
}, publisher = {
The Eurographics Association
}, ISBN = {
978-3-905673-99-9
}, DOI = {
/10.2312/PE.EuroVisShort.EuroVisShort2013.067-071
} }
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