Inclusion of Desolvation Energy into Protein–Protein Docking through Atomic Contact Potentials

Protein-protein interactions are crucial in many biological processes. Therefore, determining the structure of a protein-protein complex is valuable for understanding its molecular mechanisms and developing drugs. Molecular docking is a powerful computational tool in the prediction of protein-protein complex structures, in which a scoring function with good performance is very important. In this study, we have proposed a hybrid scoring function of atomic contact-based desolvation energies and distance-dependent interatomic potentials for protein-protein interactions, named HITScorePP, where the atomic contact desolvation energies were derived using an iterative method and the distance-dependent potentials were directly taken from our ITScorePP scoring function. Integrating the hybrid scoring function into our fast Fourier transform (FFT) based HDOCK docking scheme, the updated docking program, named HDOCK2.0, significantly improved the docking performance on the 55 newly added complexes in the protein docking benchmark 5.0 and a data set of 19 antibacterial protein complexes. HDOCK2.0 was also compared with four other state-of-the-art docking programs including Rosetta, ZDOCK3.0.2, FRODOCK3.0, ATTRACT, and PatchDock and obtained the overall best performance in binding mode predictions. These results demonstrated the accuracy of our hybrid scoring function and the necessity of included desolvation effects in protein-protein docking.