Docking to single-domain and multiple-domain proteins: Old and new challenges

The diverse selection of targets in the CAPRI experiments provides grounds for determining the limits of our rigid‐body docking program MolFit, and for extending it. We find that the sensitivity of MolFit is high, enabling it to produce reasonably accurate docking solutions when the structures undergo moderate local conformation changes upon complex formation or when the docked molecules are modeled. Yet the ranks of these solutions are sometimes too low to meet the requirements of CAPRI assessment. This indicates that the selectivity of MolFit, which was optimized for docking of unbound X‐ray structures, and which relies on the availability of external data from biochemical and bioinformatic sources, needs readjustment in order to meet the challenges presented by NMR or modeled structures. A different challenge is presented by large global conformation changes such as movements of domains. We show that such changes can be accommodated within the rigid‐body approximation by employing rigid multibody multistage docking procedures. We also address the difficulty of ranking results from 2‐body and multibody docking scans in cases in which there are no external data favoring one option over the other. Proteins 2005;60:195–201. © 2005 Wiley‐Liss, Inc.