title: Solvent accessible surface representation in a database system for protein docking.
abstract: 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 system. 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.affiliation: Institute for Computer Science, University of Munich, Germany.
authors.forename: T
authors.initials: T
authors.lastname: Seidl
authors.forename: H P
authors.initials: HP
authors.lastname: Kriegel
mesh_terms: D003196:Computer Graphics; D016208:Databases, Factual; D006454:Hemoglobins / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012984:Software; D013499:Surface Properties
chemical_list: D006454:Hemoglobins; D011506:Proteins