PlayMolecule Glimpse: Understanding Protein–Ligand Property Predictions with Interpretable Neural Networks
Alejandro Varela‐Rial, Iain Maryanow, Maciej Majewski, Stefan Doerr, Nikolai Schapin, José Jiménez-Luna, Gianni De Fabritiis · Journal of Chemical Information and Modeling · 2022
High Resolution Image Download MS PowerPoint Slide Deep learning has been successfully applied to structure-based protein–ligand affinity prediction, yet the black box nature of these models raises some questions. In a previous study, we presented K DEEP, a convolutional neural network that predicted the binding affinity of a given protein–ligand complex while reaching state-of-the-art performance. However, it was unclear what this model was learning. In this work, we present a new application to visualize the contribution of each input atom to the prediction made by the convolutional neural network, aiding in the interpretability of such predictions. The results suggest that K DEEP is able to learn meaningful chemistry signals from the data, but it has also exposed the inaccuracies of the current model, serving as a guideline for further optimization of our prediction tools.