Classification of protein complexes based on docking difficulty.

Based on the results of several groups using different docking methods, the key properties that determine the expected success rate in protein-protein docking calculations are measures of conformational change, interface area, and hydrophobicity. A classification of protein complexes in terms of these measures provides a prediction of docking difficulty. This classification is used to study the targets of the CAPRI docking experiment. Results show that targets with a moderate expected difficulty were indeed predicted well by a number of groups, whereas the use of additional a priori information was necessary to obtain good results for some very difficult targets. The analysis indicates that CAPRI and other relatively large-scale docking studies represent very important steps toward understanding the capabilities and limitations of current protein-protein docking methods.