Both our group and our ClusPro server were the best performers in the latest rounds of the CAPRI

CAPRI (Critical Assessment of Predicted Interactions) is a community-wide experiment devoted to the prediction of protein complexes based on the structures of the component proteins ( The results for targets 29-42 were evaluated at the Fourth CAPRI Evaluation Meeting in Barcelona on December 9-11, 2009, for 63 predictor groups and 10 automated docking servers ( Our team was found to have the best performance in both categories. The complete set of slides by the assessors is available for download.

The summary of the results is also shown below. For each predictor group, the table shows the number of acceptable or better predictions, and among those the number of high quality models, indicated by three stars, as well as the number of medium quality solutions, indicated by two stars. According to this table, a number of groups made 6 successful predictions, and thus our group distinguished itself only by the slightly higher number of high or medium quality models. However, together with the performance of the ClusPro automated server this result represents a real breakthrough. By definition, servers can use only the atomic coordinates of two component proteins, and no literature or other data that are available to human predictors. Nevertheless, ClusPro outperformed not only the other 9 servers, but also 53 of the 63 participating groups! According to Dr. Shoshana Wodak, head of CAPRI assessment team, an automated server was able to compete with human predictors for the first time in CAPRI‚Äôs history. 

The best solutions provided by ClusPro were further refined higher accuracy, again without the use of additional information. Accordingly, ours was the only group obtaining good results for Target T39 on which incorrect experimental data have been published, misleading all other predictors. Although the present web-based version of ClusPro does not perform the computationally very demanding refinement step, it will be included when appropriate computational resources will be available. Thus, our results in the latest round of CAPRI indicate the feasibility of high accuracy ab initio protein-protein docking for a substantial fraction of proteins.  In addition, the high computational efficiency of the initial docking and the increasing number of protein structures will enable us to solve problems in systems biology such as the validation of putative protein-protein interaction networks. 

The ClusPro 2.0 protein-protein docking server is available at

Assessment of CAPRI Predictions 2009

Barcelona, December 9-11, 2009


 GroupTotal / High / Medium
1S. Vajda (Boston University, Boston, MA)6/4***/2**
2M. Zacharias (Jacobs University, Bremen, Germany)6/4***/1**
3X. Zou (University of Missouri, Columbia, MO)6/3***/2**
4-5M. Eisenstein (Weizmann Institute, Rehovot, Israel)6/3***/1**
 H. Wolfson (Tel Aviv University, Tel Aviv, Israel) 
6-7Z. Weng (U. of Massachussets, Worcester, MA)6/2***/2**
 H-X. Zhou (Florida State U., Tallahassee, FL) 
8A. Bonvin (Utrecht University, the Netherlands)6/1***/4**
9CLUSPRO (server, Vajda group, Boston University, MA)5/1***/3**
10J. Fernandez-Recio (Barcelona Supercomputing C., Spain)5/2**
11J. Gray (John Hopkins U., Baltimore, MD)4/2***/1**
12-14 P. Bates (Cancer Research Inst., London, UK)4/1***/1**
C. Camacho (University of Pittsburgh, PA) 
 HADDOCK (server, Bonvin group, Utrecht University) 
15-16 H. Nakamura (Osaka University, Osaka, Japan)3/2***/1**
D. Baker (U. of Washington, Seattle, WA) 
17C-X. Wang (Beijing U. of Technology, Beijing, China)3/1***/1**
18D. Ritchie (INRIA, Nancy, France)3/3**
19-21 GRAMM-X (server, Vakser group, U. of Kansas, KS)2/2***
M. Takeda-Shitaka (Kitasato University, Tokyo, Japan) 
 Y. Xiao (Huazhong U. Science and Techology, Wuhan, China) 
22-24 A. Tovchigrechko (J. Craig Venter Institute, Rockville, MD)2/1***/1**
L. Ten Eyck (UC San Diego, San Diego, CA)  
 I. Vakser (U. of Kansas, Lawrence, KS) 


1CLUSPRO (Vajda group, Boston University, Boston MA)5/1***/3**
2HADDOCK (Bonvin group, Utrecht University, the Netherlands)4/1***/1**
3GRAMM-X (Vakser group, U. of Kansas, Lawrence, KS)2/2***
4SKE-DOCK (Takeda-Shitaka group, Kitasato U., Japan)2/1***
5PatchDock, FiberDock, FireDock (Wofson group, Tel Aviv U.)1/1***
6TOP DOWN (Zacharias group, Jacobs U., Bremen, Germany)1/1**
7-9HEX (Ritchie group, Nancy, France)0
 SmoothDock (Camacho group, U. Pittsburgh, US) 
 3D-Garden (Sternberg group, Imperial College, London, UK)