KDEEP: Protein-Ligand Absolute Binding Affinity Prediction via 3D-Convolutional Neural Networks

Accurately predicting protein-ligand binding affinities is an important problem in computational chemistry since it can substantially accelerate drug discovery for virtual screening and lead optimization. We propose here a fast machine-learning approach for predicting binding affinities using state-of-the-art 3D-convolutional neural networks and compare this approach to other machine-learning and scoring methods using several diverse data sets. The results for the standard PDBbind (v.2016) core test-set are state-of-the-art with a Pearson's correlation coefficient of 0.82 and a RMSE of 1.27 in pK units between experimental and predicted affinity, but accuracy is still very sensitive to the specific protein used. K-DEEP is made available via PlayMolecule.org for users to test easily their own protein-ligand complexes, with each prediction taking a fraction of a second. We believe that the speed, performance, and ease of use of K-DEEP makes it already an attractive scoring function for modern computational chemistry pipelines.