Visualizing the dual space of biological molecules

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 Asp, and the ammonia channel in the hisH–hisF complex of imidazole glycerol phosphate synthase

Visualizing the Dual Space of Biological Molecules Computational Biology and Chemistry

An important part of protein structure characterization is the determiniation 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 and within biological molecules. 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 Asp, and the ammonia channel in the hisH-hisF complex of imidazole glycerol phosphate synthase. Preprint submitted to Elsevier Science 18 November 2005