Automatic Generated Test-Sets Database for Protein-Protein Docking(AGT-SDP)

Automatic Generated Test-Sets Database for Protein-Protein Docking (AGT-SDP) is a database providing test cases for protein-protein docking.

Introduction:In unbound protein--protein docking, the complex of two proteins is predicted using the unbound conformations of the proteins (Halperin et al.,2002). For testing of docking algorithms, two unbound proteins which form a known complex have to be identified, so that the result of the docking algorithm can be compared to the known complex. For the identification of test cases, the structures taken from the PDB have to be classified as unbound proteins or complexes and unbound proteins with a 100% sequence identity to one complex part have to be searched. By now, most groups use handpicked test sets. The largest collection of test cases used so far is described by Chen et al. (Chen et al.,2003) and contains 31 test cases for unbound docking. Because of the exponential growth of available protein structures in the PDB, automatic generation of test cases will become more and more important in the future.

To use this service please click on the Submission button. The manual page gives information how to use this database and provide some information on the methods used to generate test sets. If you encounter problems using this service please use the contact adress provided in the contact section. If you use data set composed by this service please cite the reference listed here.

We recently added support for submitting your own test cases. Please use the Add Test Case form to add your test cases. In order to verify the provided data and to give other users a reference to the origin of this data, we require to submit a reference citing the submitted data.

This database has been created in the context of the local developed docking system ELMAR and will be used in different associated research projects.