Ludwig-Maximilians-Universität München, Institut für Informatik
Technical Report 95-07
- TITLE:
-
Solvent Accessible Surface Representation in a Database System for Protein Docking
- DATE:
-
May 1995
- AUTHORS:
- Thomas Seidl
- Hans-Peter Kriegel
- {kriegel | seidl}@informatik.uni-muenchen.de
- Institut für Informatik
- Universität München
- Leopoldstr. 11B
- D-80802 München (Germany)
- KEYWORDS:
-
Molecular surface representation, planar graphs, surface approx-
imation, local shape index, efficient query processing, spatial
database systems, 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 multi-step
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.
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