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Bioinformatics Advance Access originally published online on October 12, 2004
Bioinformatics 2005 21(5):683-684; doi:10.1093/bioinformatics/bti061
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Database driven test case generation for protein–protein docking

Frank Zöllner *, Steffen Neumann , Franz Kummert and Gerhard Sagerer

Applied Computer Science, Faculty of Technology, Bielefeld University D-33594 Bielefeld, Germany

*To whom correspondence should be addressed.

Summary: We present a method for automatic test case generation for protein–protein docking. A consensus-type approach is proposed processing the whole PDB and classifying protein structures into complexes and unbound proteins by combining information from three different approaches (current PDB-at-a-glance classification, search of complexes by sequence identical unbound structures and chain naming). Out of this classification test cases are generated automatically. All calculations were run on the database. The information stored is available via a web interface. The user can choose several criteria for generating his own subset out of our test cases, e.g. for testing docking algorithms.

Availability: http://bibiserv.techfak.uni-bielefeld.de/agt-sdp/

Contact: fzoellne{at}techfak.uni-bielefeld.de


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