Solvent Accessible Surface Representation in a Database System for Protein Docking

Protein docking is a new and challenging application for query processing in database systems. Our architecture for an efficient support of docking queries is based on the multistep query processing paradigm, a technique well-known from spatial database systems. Along with physicochemical parameters, the geometry of the molecules plays a fundamental role for docking retrieval. Thus, 3D structures and 3D surfaces of molecules are basic objects in molecular databases. We specify a molecular surface representation based on topology, define a class of neighborhood queries, and sketch some applications with respect to the docking problem. We suggest a patch-based data structure called the TriEdge structure, first, to efficiently support topological query processing, and second, to save space in comparison to common planar graph representations such as the quad-edge structure. In analogy to the quad-edge structure, the TriEdge structure has an algebraic interface and is implemented via complex pointers. However, we achieve a reduction of the space requirement by a factor of four. Finally, we investigate the time performance of our prototype.

Authors: Seidl T., Kriegel H.-P.
Published in: Proc. 3rd Int. Conf. on Intelligent Systems for Molecular Biology (ISMB 1995), Cambridge, UK. AAAI Press
Publisher: AAAI
Sprache: EN
Jahr: 1995
Seiten: 350-358
ISBN: 0-929280-83-0
Konferenz: ISMB
Typ: Tagungsbeiträge
Forschungsgebiet: Exploration of Multimedia Databases