In rounds 3–5 of CAPRI, the community-wide experiment on the comparative evaluation of protein–protein docking for structure prediction, we applied the 3D-Dock software package to predict the atomic structures of nine biophysical interactions. This approach starts with an initial grid-based shape complementarity search. The product of this is a large number of potential interacting conformations that are subsequently ranked by interface residue propensities and interaction energies. Refinement through detailed energetics and optimization of side-chain positions using a rotamer library is also performed. For rounds 3, 4, and 5 of the CAPRI evaluation, where possible, we clustered functional residues on the surfaces of the monomers as an indication of binding sites, using sequence based evolutionary conservations. In certain targets this provided a very useful tool for identifying the areas of interaction. During round 5, we also applied the techniques of side-chain trimming and geometrical clustering described in the literature. Of the nine target complexes in rounds 3–5, we predicted conformations that contained at least some correct contact residues for seven of these systems. For two of the targets, we submitted predictions that were considered as medium-quality. These were a nidogen–laminin complex for target 8 (T08) and a serine-threonine phosphatase bound to a targeting subunit (T14). For a further three target systems, we produced models that were rated as acceptable predictions. Proteins 2005;60:281–288. © 2005 Wiley-Liss, Inc.