Leak Proof PDBBind: A Reorganized Data Set of Protein–Ligand Complexes for More Generalizable Binding Affinity Prediction

The majority of machine learning scoring functions used in drug discovery for predicting protein-ligand binding poses and affinities have been trained on the PDBBind data set. However, it is unclear whether these new scoring functions are actually an improvement over traditional models since often the training and test sets are cross-contaminated with proteins and ligands with high similarity, and hence, they may not perform comparably well in binding prediction of unrelated protein-ligand complexes. In this work, we have carefully prepared a new split of the PDBBind data set to control for data leakage, defined as proteins and ligands with high sequence and structural similarity. The resulting leak-proof (LP)-PDBBind data are used to retrain four popular SFs: AutoDock Vina, Random Forest (RF)-Score, InteractionGraphNet (IGN), and DeepDTA, to better test their capabilities when applied to new protein-ligand complexes. In particular, we have formulated a new independent data set, BDB2020+, by matching high-quality binding free energies from BindingDB with cocrystallized ligand-protein complexes from the PDB that have been deposited since 2020. Based on all of the benchmark results, the retrained models using LP-PDBBind consistently perform better, with IGN especially being recommended for scoring and ranking applications for new protein-ligand systems.