Extraction of Robust Voids and Pockets in Proteins

Sridharamurthy, Raghavendra; Doraiswamy, Harish; Patel, Siddharth; Varadarajan, Raghavan; Natarajan, Vijay

Extraction of Robust Voids and Pockets in Proteins

Files

067-071.pdf (984.62 KB)

short-0117-file1.pdf (1.41 MB)

Date

2013

Authors

Sridharamurthy, Raghavendra
Doraiswamy, Harish
Patel, Siddharth
Varadarajan, Raghavan
Natarajan, Vijay

Publisher

The Eurographics Association

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).

        @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
}
}