BDOCK

BDOCK: a novel enzyme-inhibitor docking algorithm based on the degree of burial and conservation of surface residues

From here you can download a protein-protein docking programme called BDOCK which is very fast for protein-protein docking. In the initial stage of docking, BDOCK takes the degree of burial and conservation of surface residues into account, which works very well for enzyme-inhibitor complexes. This protein docking programme is developed using BALL (Biochemical Algorithm Library) based on the Fast Frourie Transform method.

If you have any questions about this programm, please contact me at bhuang@biotec.tu-dresden.de.

Reference:

Bingding Huang and Michael Schroeder (2005), Using residue propensities and tightness of fit to improve rigid-body protein-protein docking. In Matthias Rarey, Andrew Torda, Stefan Kurtz, and Ute Willhoeft, editors, Proceedings of German Bioinformatics Conference. Pages:159-173, Springer. PDF.
Bingding Huang and Michael Schroeder(2008), Using protein binding site to improve protein-protein docking, Gene, Epub 1;422(1-2):14-2. link