ClusPro (http://nrc.bu.edu/cluster) represents the first fully automated, 
web-based program for the computational docking of protein structures. Users may 
upload the coordinate files of two protein structures through ClusPro's web 
interface, or enter the PDB codes of the respective structures, which ClusPro 
will then download from the PDB server (http://www.rcsb.org/pdb/). The docking 
algorithms evaluate billions of putative complexes, retaining a preset number 
with favorable surface complementarities. A filtering method is then applied to 
this set of structures, selecting those with good electrostatic and desolvation 
free energies for further clustering. The program output is a short list of 
putative complexes ranked according to their clustering properties, which is 
automatically sent back to the user via email.