Molecular surface representation, planar graphs, surface approx- imation, local shape index, efficient query processing, spatial database systems, protein docking.
Protein docking is a new and challenging application for query processing in 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. 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.