Short communication: Visualizing the dual space of biological molecules

  • Authors:
  • John Eargle;Zaida Luthey-Schulten

  • Affiliations:
  • 607 South Mathews Ave., Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States;607 South Mathews Ave., Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States and A544 CLSL, Box 41-6, 600 S. Mathews Ave., D ...

  • Venue:
  • Computational Biology and Chemistry
  • Year:
  • 2006

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Abstract

An important part of protein structure characterization is the determination of excluded space such as fissures in contact interfaces, pores, inaccessible cavities, and catalytic pockets. We introduce a general tessellation method for visualizing the dual space around, within, and between biological molecules. Using Delaunay triangulation, a three-dimensional graph is constructed to provide a displayable discretization of the continuous volume. This graph structure is also used to compare the dual space of a system in two different states. Tessellator, a cross-platform implementation of the algorithm, is used to analyze the cavities within myoglobin, the protein-RNA docking interface between aspartyl-tRNA synthetase and tRNA^A^s^p, and the ammonia channel in the hisH-hisF complex of imidazole glycerol phosphate synthase.