Extraction of robust voids and pockets in proteins.

Raghavendra Sridharamurthy, Talha Bin Masood, Harish Doraiswamy, Siddharth Patel, Raghavan Varadarajan and Vijay Natarajan.
In Visualization in Medicine and Life Sciences III.
Lars Linsen, Hans-Christian Hege, and Bernd Hamann (Eds.)
Springer-Verlag, Mathematics and Visualization Series, 2016, 329-349.
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Abstract

Voids and pockets in a protein, collectively called as cavities, refer to empty spaces that are enclosed by the protein molecule. Existing methods to compute, measure, and visualize the cavities 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, cavities are represented as subsets of the weighted Delaunay triangulation of atom centres. A novel notion of (ϵ,π)-stable cavities helps identify cavities that are stable even after perturbing the atom radii by a small value. An efficient method is described to compute these stable cavities for a given input pair of values (ϵ,π). This approach is used to identify potential pockets and channels in protein structures.

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