Welcome to the Cross Docking Benchmark server. This server has been created as a useful benchmark for crossdocking using the Targets listed in DUD-E as a reference. The completed benchmark contains:
4,399 ligand and receptor structures homologous to one of 95 targets, an average of 46 ligands per target.
Ligand-receptor complexes are separated into ligand.pdb and receptor.pdb files, each aligned to a reference receptor for convenience.
All files are "docking ready".
Docking results based on methods shown to be top-of-the-line in D3R Grand Challenges for pose prediction and affinity ranking.1,2,3
1. Ye, Zhaofeng, et al. "Optimal strategies for virtual screening of induced-fit and flexible target in the 2015 D3R Grand Challenge." Journal of computer-aided molecular design 30.9 (2016): 695-706.
2. Wingert, Bentley M., Rick Oerlemans, and Carlos J. Camacho. "Optimal affinity ranking for automated virtual screening validated in prospective D3R grand challenges." Journal of computer-aided molecular design 32.1 (2018): 287-297.
3. Wingert, Bentley M., and Carlos J. Camacho. "Improving small molecule virtual screening strategies for the next generation of therapeutics." Current opinion in chemical biology 44 (2018): 87-92.
The benchmark files may be downloaded as the default benchmark or you may generate your own benchmark using targets of interest.
The Cross Docking Benchmark is a product of the Camacho Laboratory in the Department of Computational and Systems Biology at the The University of Pittsburgh.
Cross Docking Benchmark is provided by the Camacho Laboratory at University of Pittsburgh and is developed by Shayne Wierbowski of the University of Scranton and Jim Zheng of the University of Pittsburgh.
Scripts and website content © 2023 Shayne Wierbowski - University of Scranton. Website content © 2023 Jim Zheng - University of Pittsburgh. All rights reserved.