Visualizing the dual space of biological molecules

John Eargle, Zaida Luthey-Schulten
2006 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
more » ... tates. 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.
doi:10.1016/j.compbiolchem.2006.01.004 pmid:16675303 fatcat:xi6ayftsnbc6jeodwpgueapbmu