My current research interests include the improvement of our protein-protein docking methodology by increasing the effectiveness of DOT, and improving the filtering methods and scoring functions used. Eventually, I would like to incorporate homology modeling into standard protein-protein docking.
In order to evaluate the current status of the protein-protein docking field, the CAPRI experiment came to life. However, one problem with the structure of the experiment is that researchers are allowed to use biochemical information in order to make their predictions, and this manual intervention hasn't clearly illustrated the status of the docking field.
To offset this problem, we developed the first fully-automated, web server for protein-protein docking, ClusPro. ClusPro has participated in Rounds 3-5 of CAPRI with success relative to the field, and our results can be seen here.
Target 10 of CAPRI brought a new challenge to the docking field, as three individual monomers were needed to construct the final model, whereas traditional docking only requires two monomers. Thus, we have developed a methodology which constructs homo-N-mers (where N ranges from 2 through 6) using symmetry relationships between the docked monomers to construct the final multimer.
Publications:Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: An FFT-based protein docking program with pairwise potentials Proteins. 2006 Aug 24
Comeau SR, Vajda S, Camacho CJ. Performance of the first protein docking server ClusPro in CAPRI rounds 3-5. Proteins, 2005 Aug 1;60(2):239-44
Comeau SR, Camacho CJ. Predicting multi-protein assemblies: N-mers as a primer. J. of Struct. Biol. 2005 Jun 150(3):233-44
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W96-9.
Comeau SR, Gatchell DW, Vajda S, Camacho CJ. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics. 2004 Jan 1;20(1):45-50.
Prasad JC, Comeau SR, Vajda S, Camacho CJ. Consensus alignment for reliable framework prediction in homology modeling. Bioinformatics. 2003 Sep 1;19(13):1682-91.
Shakhnovich BE, Harvey JM, Comeau S, Lorenz D, DeLisi C, Shakhnovich E. ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations. BMC Bioinformatics. 2003 Sep 02;4(1):34.