ClusPro: Fully automated docking and discrimination servers

In 2004 we have implemented the first three steps of our multistage algorithm in ClusPro, the first fully automated protein-protein docking and discrimination server. ClusPro 1.0 includes (1) rigid body docking by DOT or ZDOCK; (2) selection of 2000 docked structures with favorable desolvation and electrostatics, (3) clustering of the retained complexes using a pairwise RMSD criterion, and reporting the centers of the 30 largest clusters. Since the server does not provide further discrimination, the most reasonable use of docking at this point is to consider the top predictions as putative structural models, and employ low resolution or non-structural experiments such as cross-linking or site-directed mutagenesis for selecting the correct model.

By September 2007, the server performed 13,915 docking calculations for 1,824 outside users. We have found over 35 research papers that used ClusPro as an important part of the methodology.

We have recently released the beta version of ClusPro 2.0. The main change is that the new server docks the two proteins using the improved docking program PIPER.