CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock

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Abstract
CAPRI Rounds 3, 4, and 5 are the first public test of the published RosettaDock algorithm. The targets cover a wide range of sizes and shapes. For most targets, published biological information indicated the region of the binding site on at least one docking partner. The RosettaDock algorithm produced high accuracy predictions for three targets, medium‐accuracy predictions for two targets, and an acceptable prediction for one target. RosettaDock predicted all five targets with less than 450 residues to high or medium accuracy, but it predicted only one of seven targets with above 450 residues to acceptable accuracy. RosettaDock's high‐accuracy predictions for small to moderately large targets reveal the predictive power and fidelity of the algorithm, especially the high‐resolution refinement and scoring protocol. In addition, RosettaDock can predict complexes from at least one homology‐modeled docking partner with comparable accuracy to unbound cases of similar size. Larger targets present a more intensive sampling problem, and some large targets present repulsive barriers to entering the binding site. Ongoing improvements to RosettaDock's low‐resolution search may alleviate this problem. This first public test suggests that RosettaDock can be useful in a significant range of applications in biochemistry and cell biology. Proteins 2005;60:181–186.