Visualizing the dual space of biological molecules

Research output: Contribution to journalArticle

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 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
Volume30
Issue number3
DOIs
StatePublished - Jun 1 2006

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Keywords

  • Delaunay triangulation
  • Protein/tRNA interface
  • Tessellation

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics

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