Database driven test case generation for protein-protein docking.
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.


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


BACKGROUND
fzoellne@techfak.uni-bielefeld.de.
Applied Computer Science, Faculty of Technology, Bielefeld University D-33594 Bielefeld, Germany. fzoellne@techfak.uni-bielefeld.de
Frank
F
Zöllner
Steffen
S
Neumann
Franz
F
Kummert
Gerhard
G
Sagerer
D000465:Algorithms; D019985:Benchmarking / Q000379:methods / Q000592:standards; D001665:Binding Sites; D030562:Databases, Protein; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods* / Q000592:standards; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000648:ultrastructure; D020539:Sequence Analysis, Protein / Q000379:methods* / Q000592:standards
D011506:Proteins