Welcome to the ZDOCK Conv3D homepage. This is a project to integrate the 3D convolution library, Conv3D (provided by Dr. Yuichiro Hourai of the Computational Biology Research Center, AIST, Japan), into the ZDOCK protein-protein docking program (developed by our laboratory). We subsequently made several changes to the ZDOCK algorithm to dynamically adjust the positioning and orientation of input proteins to more efficiently utilize grid space, resulting in further improvements in running time and memory usage. We have integrated these improvements into two versions of ZDOCK: ZDOCK 2.3 and ZDOCK 3.0. These optimized versions of ZDOCK are named ZDOCK 2.3.2 and ZDOCK 3.0.2, respectively.

Downloads of the ZDOCK 2.3.2 and ZDOCK 3.0.2 programs are available for Linux, IBM Blue Gene, and Mac OS X platforms. They are freely available to all academic and non-profit users.

Decoy Sets
Downloadable sets of docking results from ZDOCK 2.3.2 and ZDOCK 3.0.2 for Benchmark 4.0, to help users to test and train their own algorithms.

Java-based interface to generate structures of ZDOCK predictions from a ZDOCK output file.

If you use ZDOCK 3.0.2 or 2.3.2 (or currently obsolete versions 3.0.1 or 2.3.1) in your work, please cite this paper:
Pierce BG, Hourai Y, Weng Z, 2011 Accelerating Protein Docking in ZDOCK Using an Advanced 3D Convolution Library. PLoS One 6(9): e24657.

Thanks to Dr. Yuichiro Hourai for providing the library and support for integrating it into ZDOCK.
Also, thanks to the Scientific Computing Group at Boston University for computing resources.

Please send suggestions to: Brian Pierce