Predicting Protein-protein Interactions with DrugScorePPI: Docking, Scoring, and in silico Alanine-scanning

Protein-protein complexes play key roles in many cellular processes. Therefore, knowledge of the 3D structure of protein-complexes is of fundamental importance. A key goal in protein-protein docking is to identify near-native protein-complex structures using an appropriate scoring function. In this work, we tested our recently developed knowledge-based approach DrugScore PPI (I) for identifying hotspots in protein-protein interfaces, (II) as a scoring function for rescoring a large dataset of pre-generated protein-protein docking decoys, and (III) as an objective function in combination with a fast spherical harmonics-based protein-protein docking tool for predicting 3D structures of protein-protein complexes.