TY - JOUR
T1 - Visualizing the dual space of biological molecules
AU - Eargle, John
AU - Luthey-Schulten, Zaida
N1 - Funding Information:
We would like to thank Klaus Schulten for suggesting the self-organizing neural network algorithm for tessellation, Rommie Amaro for the SMD trajectories and HOLE pore determination of the hisH–hisF complex, and Carl Woese for the AspRS sequence alignments used in the evolutionary profiles. We would also like to acknowledge the support of the NIH Molecular Biophysics Training Grant PHS5T32GM08276 and NSF grant MCB04-46227.
PY - 2006/6
Y1 - 2006/6
N2 - 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.
AB - 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.
KW - Delaunay triangulation
KW - Protein/tRNA interface
KW - Tessellation
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U2 - 10.1016/j.compbiolchem.2006.01.004
DO - 10.1016/j.compbiolchem.2006.01.004
M3 - Article
C2 - 16675303
AN - SCOPUS:33744486941
SN - 1476-9271
VL - 30
SP - 219
EP - 226
JO - Computational Biology and Chemistry
JF - Computational Biology and Chemistry
IS - 3
ER -