THE STUDY OF THE SCORING FUNCTION IN PROTEIN-PROTEIN DOCKING
蛋白质-蛋白质对接中打分函数的研究

Binding free energy potentials, combining molecular mechanics with empirical solvation and entropic terms, are used to discriminate near-native conformations from slightly misdocked protein-protein decoys. It is of interest to determine the contributions of individual binding free energy terms and their combinations to the discriminative power of the potential. This is achieved in terms of quantitative measure of the correlation coefficient between binding free energy and the root mean square deviation (RMSD) of backbone atoms from the native complex structure. From the results, the discrimination improves if the binding free energy expression includes the electrostatic energy and an empirical solvation term, with the structure-based atomic contact potential (ACE) providing much better discrimination than the atomic solvation parameter model (ASP). Moreover, obvious improvement is obtained when using the modified atomic contact potential is used. By scoring test for 36 protein-protein docking cases, the results further indicate that the combination of the electrostatic energy and the modified atomic contact potential (ACE) is of much better discriminative power and can be used to score the putative binding modes in protein-protein docking.