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Nucleic Acids Research 2004 32(Web Server Issue):W96-W99; doi:10.1093/nar/gkh354
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© 2004, the authors
Nucleic Acids Research, Vol. 32, Web Server issue © Oxford University Press 2004; all rights reserved

ClusPro: a fully automated algorithm for protein–protein docking

Stephen R. Comeau1, David W. Gatchell2, Sandor Vajda1,2 and Carlos J. Camacho1,2,*

1 Bioinformatics Graduate Program and 2 Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA

* To whom correspondence should be addressed. Tel: +1 617 353 4842; Email: ccamacho{at}bu.edu

Received February 14, 2004; Accepted February 23, 2004

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.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated.


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