A Comprehensive Survey of Scoring Functions for Protein Docking Models

Background: While protein-protein docking is fundamental to our understanding of how proteins interact, scoring protein-protein complex conformations is a critical component of successful docking programs. Without accurate and efficient scoring functions to differentiate between native and non-native binding complexes, the accuracy of current docking tools cannot be guaranteed. Although many innovative scoring functions have been proposed, a good scoring function for docking remains elusive. Deep learning models offer alternatives to using explicit empirical or mathematical functions for scoring protein-protein complexes. Results: In this study, we perform a comprehensive survey of the state-of-the-art scoring functions by considering the most popular and highly performant approaches, both classical and deep learning-based, for scoring protein-protein complexes. Conclusions: We evaluate the strengths and weaknesses of classical and deep learning-based approaches across seven public and popular datasets to aid researchers in understanding the progress made in this field. Keywords: Computational structural biology, Protein-protein interactions, Scoring functions, Molecular docking, Deep learning, Protein surface properties