Visualizing the dual space of biological molecules

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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 tRNAAsp, and the ammonia channel in the hisH-hisF complex of imidazole glycerol phosphate synthase.

Original languageEnglish (US)
Pages (from-to)219-226
Number of pages8
JournalComputational Biology and Chemistry
Issue number3
StatePublished - Jun 2006


  • Delaunay triangulation
  • Protein/tRNA interface
  • Tessellation

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics


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