Comparison of DNA-protein pair potentials for model selection.

*CL and EN denote two scoring schemes using our DNA-protein interfacial energy function with and without clustering, respectively. QCRes and QCAA designate schemes using quasichemical pair potentials at the residue level with a single distance cutoff and at the all-atom level with multiple distance bins, respectively. The RAPDF scheme uses a scoring function proposed by Robertson and Varani [30]. For each scheme, the results of the best of top five ranked models are shown for the predictions on the APO/HOLO sets. †Mean and standard deviation of MCC are shown for the binding site predictions. ‡The number (percentage) of proteins for which the predicted complex model are acceptable according to the CAPRI criteria.