TRScore: a 3D RepVGG-based scoring method for ranking protein docking models

Abstract

Abstract Motivation Protein–protein interactions (PPI) play important roles in cellular activities. Due to the technical difficulty and high cost of experimental methods, there are considerable interests towards the development of computational approaches, such as protein docking, to decipher PPI patterns. One of the important and difficult aspects in protein docking is recognizing near-native conformations from a set of decoys, but unfortunately, traditional scoring functions still suffer from limited accuracy. Therefore, new scoring methods are pressingly needed in methodological and/or practical implications. Results We present a new deep learning-based scoring method for ranking protein–protein docking models based on a 3D RepVGG network, named TRScore. To recognize near-native conformations from a set of decoys, TRScore voxelizes the protein–protein interface into a 3D grid labeled by the number of atoms in different physicochemical classes. Benefiting from the deep convolutional RepVGG architecture, TRScore can effectively capture the subtle differences between energetically favorable near-native models and unfavorable non-native decoys without needing extra information. TRScore was extensively evaluated on diverse test sets including protein–protein docking benchmark 5.0 update set, DockGround decoy set, as well as realistic CAPRI decoy set and overall obtained a significant improvement over existing methods in cross-validation and independent evaluations. Availability and implementation Codes available at: https://github.com/BioinformaticsCSU/TRScore