Improving Protein–Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM–GBSA Scoring Function

Protein-peptide docking, which predicts the complex structure between a protein and a peptide, is a valuable computational tool in peptide therapeutics development and the mechanistic investigation of peptides involved in cellular processes. Although current peptide docking approaches are often able to sample near-native peptide binding modes, correctly identifying those near-native modes from decoys is still challenging because of the extremely high complexity of the peptide binding energy landscape. In this study, we have developed an efficient postdocking rescoring protocol using a combined scoring function of knowledge-based ITScorePP potentials and physics-based MM-GBSA energies. Tested on five benchmark/docking test sets, our postdocking strategy showed an overall significantly better performance in binding mode prediction and score-rmsd correlation than original docking approaches. Specifically, our postdocking protocol outperformed original docking approaches with success rates of 15. 8 versus 10. 5% for pepATTRACT on the Global₅7 benchmark, 5. 3 versus 5. 3% for CABS-dock on the Global₅7 benchmark, 17. 0 versus 11. 3% for FlexPepDock on the LEADS-PEP data set, 40. 3 versus 33. 9% for HPEPDOCK on the Local₆2 benchmark, and 64. 2 versus 52. 8% for HPEPDOCK on the LEADS-PEP data set when the top prediction was considered. These results demonstrated the efficacy and robustness of our postdocking protocol.