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Visualizing the dual space of biological molecules

Paper ID Volume ID Publish Year Pages File Format Full-Text
15467 1415 2006 8 PDF Available
Title
Visualizing the dual space of biological molecules
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.

Keywords
Tessellation; Protein/tRNA interface; Delaunay triangulation
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Visualizing the dual space of biological molecules
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 30, Issue 3, June 2006, Pages 219–226
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us