BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening

Abstract

Deep learning methods that predict protein-ligand binding have recently been used for structure-based virtual screening. Many such models have been trained using protein-ligand complexes with known crystal structures and activities from the PDBBind dataset. However, because PDBbind only includes 20K complexes, models typically fail to generalize to new targets, and model performance is on par with models trained with only ligand information. Conversely, the ChEMBL database contains a wealth of chemical activity information but includes no information about binding poses. We introduce BigBind, a dataset that maps ChEMBL activity data to proteins from the CrossDocked dataset. BigBind comprises 583K ligand activities and includes 3D structures of the protein binding pockets. Additionally, we augmented the data by adding an equal number of putative inactives for each target. Using this data, we developed BANANA (BAsic NeurAl Network for binding Affinity), a neural network-based model to classify active from inactive compounds, defined by a 10 μM cutoff. Our model achieved an AUC of 0.72 on BigBind’s test set, while a ligand-only model achieved an AUC of 0.59. Furthermore, BANANA achieved competitive performance on the LIT-PCBA benchmark (median EF1\% 1.81) while running 16,000 times faster than molecular docking with GNINA. We suggest that BANANA, as well as other models trained on this dataset, will significantly improve the outcomes of prospective virtual screening tasks.