Extraction of Robust Voids and Pockets in Proteins
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Date
2013
Journal Title
Journal ISSN
Volume Title
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).
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}
}