Database Systems

Docking Search in 3D Protein Databases
(BMBF joint project BIOWEPRO)

Team Leader

Prof. Dr. Hans-Peter Kriegel


Kai Aldinger
Thomas Schmidt
Thomas Seidl

Project Partner

  • Gesellschaft für Biotechnologische Forschung mbH (GBF), Braunschweig, Prof. Dr. Dietmar Schomburg, coordinator
  • University of Bielefeld, Applied Computer Science Group, Prof. Dr. Gerhard Sagerer
  • Max-Planck-Institute for Biophysical Chemistry, Göttingen, Dr. D. Mario Soumpasis


    German Ministry for Education, Science, Research, and Technology (BMBF), Strategy concept Molecular Bioinformatics

    Joint projekt Biomolecular Interactions of Proteins (BIOWEPRO)

    Munich part Development of a Molecular Surface Representation for Database Systems

    Grant no. 01 IB 307 B


    In the project BIOWEPRO, we develop new database techniques to effectively and efficiently support the 1:n-docking prediction for proteins. Our approach includes new representation and storage methods for molecular surfaces as well as new methods for similarity query processing for 3D surface segments with respect to shape similarity. The selection of segments from the database which have a similar (or complementary) 3D shape yields a set of potential docking candidates for the query protein.

    Proteins play an important role in every living organism since they are the acting instances for all fundamental processes of life like in the digestive system, metabolism, and immunosystem. The function of proteins takes place as an interaction with other molecules which is called docking.

    An important heuristic for the prediction of molecular interaction is the `key-and-lock'-principle. The docking sites of the partner molecules have a strong complementarity, especially concerning the geometry. Many docking sites may be determined solely by this complementarity geometry. Thus, the docking problem may be transformed to a search problem for complementary surface segments. While following our segmentation approach, we compute the molecular surface and extract potential docking segments for all the proteins in our database. For each of the segments, various shape representations are computed that are appropriate to support a complementarity search in the database.

    Research Topics

  • Protein Database and Molecular Surfaces
  • Similarity of 3D Surface Segments


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