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An Integrated Geometric and Topological Approach to Connecting Cavities in Biomolecules

Bin Masood, Talha and Natarajan, Vijay (2016) An Integrated Geometric and Topological Approach to Connecting Cavities in Biomolecules. In: IEEE Pacific Visualization Symposium (IEEE PacificVis), APR 19-22, 2016, Natl Taiwan Univ Sci & Technol, Taipei, TAIWAN, pp. 104-111.

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Study of cavities and channels in molecular structure is a crucial step in understanding the function of biomolecules. Current tools and techniques for extracting these structural features are sensitive to uncertainties in atomic position and radii. In this paper, we study the problem of cavity extraction in biomolecules while taking into account such uncertainties. We propose an approach that connects user-specified cavities by computing an optimal conduit within the region occupied by the molecule. The conduit is computed using a topological representation of the occupied and empty regions and is guaranteed to satisfy well defined geometric optimality criteria. Visualization of the set of all cavities with multiple linked views serves as a useful interface for interactive extraction of stable cavities. We demonstrate the utility of the proposed method in successfully identifying biologically significant pathways between molecular cavities using several case studies.

Item Type: Conference Paper
Series.: IEEE Pacific Visualization Symposium
Additional Information: Copy right for this article belongs to the IEEE, 345 E 47TH ST, NEW YORK, NY 10017 USA
Department/Centre: Division of Electrical Sciences > Computer Science & Automation
Division of Interdisciplinary Sciences > Computational and Data Sciences
Date Deposited: 03 Dec 2016 10:21
Last Modified: 11 Oct 2018 15:06
URI: http://eprints.iisc.ac.in/id/eprint/55434

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