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.