The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation.

We participated in rounds 6-12 of the critical assessment of predicted interaction (CAPRI) contest as the SKE-DOCK server and human teams. The SKE-DOCK server is based on simple geometry docking and a knowledge base scoring function. The procedure is summarized in the following three steps: (1) protein docking according to shape complementarity, (2) evaluating complex models, and (3) repacking side-chain of models. The SKE-DOCK server did not make use of biological information. On the other hand, the human team tried various intervention approaches. In this article, we describe in detail the processes of the SKE-DOCK server, together with results and reasons for success and failure. Good predicted models were obtained for target 25 by both the SKE-DOCK server and human teams. When the modeled receptor proteins were superimposed on the experimental structures, the smallest Ligand-rmsd values corresponding to the rmsd between the model and experimental structures were 3.307 and 3.324 A, respectively. Moreover, the two teams obtained 4 and 2 acceptable models for target 25. The overall result for both the SKE-DOCK server and human teams was medium accuracy for one (Target 25) out of nine targets. (c) 2007 Wiley-Liss, Inc.