Protein–protein docking: is the glass half-full or half-empty? Original Research Article

Are current docking methods capable of building complexes from putative component protein structures? Results of recent computational studies, including those of the CAPRI (Critical Assessment of Protein Interactions) competition, were used to determine the key properties for successful docking and introduce a classification of protein complexes based on docking difficulty. Enzyme–inhibitor complexes could be determined with reasonable accuracy – possibly to within a few alternative structures. Results for antigen–antibody pairs are less predictable, and data for small signaling complexes are generally poor. However, moderate amounts of experimental data can remove uncertainty and the methodology is rapidly improving. Transient complexes with large interface areas undergo substantial conformational change and are beyond the reach of current docking methods. The docking of such complexes might therefore require fundamentally new approaches.