Learning from Docked Ligands: Ligand-Based Features Rescue Structure-Based Scoring Functions When Trained On Docked Poses

Machine learning scoring functions for protein-ligand binding affinity have been found to consistently outperform classical scoring functions when trained and tested on crystal structures of bound protein-ligand complexes. However, it is less clear how these methods perform when applied to docked poses of complexes.

We explore how the use of docked, rather than crystallographic, poses for both training and testing affects the performance of machine learning scoring functions. Using the PDBbind Core Sets as benchmarks, we show that the performance of a structure-based machine learning scoring function trained and tested on docked poses is lower than that of the same scoring function trained and tested on crystallographic poses. We construct a hybrid scoring function by combining both structure-based and ligand-based features, and show that its ability to predict binding affinity using docked poses is comparable to that of purely structure-based scoring functions trained and tested on crystal poses. Despite strong performance on docked poses of the PDBbind Core Sets, we find that our hybrid scoring function fails to generalise to anew data set, demonstrating the need for improved scoring functions and additional validation benchmarks.

Code and data to reproduce our results are available from https://github.com/oxpig/learning-from-docked-poses.