AUTHOR=Meli Rocco , Morris Garrett M. , Biggin Philip C. TITLE=Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review JOURNAL=Frontiers in Bioinformatics VOLUME=2 YEAR=2022 URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2022.885983 DOI=10.3389/fbinf.2022.885983 ISSN=2673-7647 ABSTRACT=

The rapid and accurate in silico prediction of protein-ligand binding free energies or binding affinities has the potential to transform drug discovery. In recent years, there has been a rapid growth of interest in deep learning methods for the prediction of protein-ligand binding affinities based on the structural information of protein-ligand complexes. These structure-based scoring functions often obtain better results than classical scoring functions when applied within their applicability domain. Here we review structure-based scoring functions for binding affinity prediction based on deep learning, focussing on different types of architectures, featurization strategies, data sets, methods for training and evaluation, and the role of explainable artificial intelligence in building useful models for real drug-discovery applications.