A Fast and Interpretable Deep Learning Approach for Accurate Electrostatics-Driven p<i>K</i><sub>a</sub> Predictions in Proteins
Pedro B. P. S. Reis, Marco Bertolini, Floriane Montanari, Walter Rocchia, Miguel Machuqueiro, Djork-Arné Clevert
Abstract
Existing computational methods for estimating pKa values in proteins rely on theoretical approximations and lengthy computations. In this work, we use a data set of 6 million theoretically determined pKa shifts to train deep learning models, which are shown to rival the physics-based predictors. These neural networks managed to infer the electrostatic contributions of different chemical groups and learned the importance of solvent exposure and close interactions, including hydrogen bonds. Although trained only using theoretical data, our pKAI+ model displayed the best accuracy in a test set of ∼750 experimental values. Inference times allow speedups of more than 1000× compared to physics-based methods. By combining speed, accuracy, and a reasonable understanding of the underlying physics, our models provide a game-changing solution for fast estimations of macroscopic pKa values from ensembles of microscopic values as well as for many downstream applications such as molecular docking and constant-pH molecular dynamics simulations.