Scoring Function for the Other-type Protein Complexe

Abstract Based on the observation that different complexes have distinctive chemo-physical characters at interfaces, a specific scoring function was designed to select the effective structures in protein-protein docking procedure for the Other-type protein complexes that are difficult to predict. This scoring function was composed of the atomic contact energy (EACE), van der Waals, and electrostatic interaction energies. The weight of each term was obtained by the multiple linear regression approach. The test result on 17 Other-type complexes from CAPRI benchmark 1 demonstrated that the combinatorial scoring function can delineate the interaction feature of the Other-type complexes, reflect the energy change during the complex formation, and have a certain capacity to discriminate effective structures from numbers of the docked modes. Compared with the residue pair potential (RP), the combinatorial score was found to have a higher success rate. Through ranking the predicted models of the two targets in CARPI round 8, the combinatorial score also exhibits a higher degree of accuracy in distinguishing the effective association modes.