ET‐score: Improving Protein‐ligand Binding Affinity Prediction Based on Distance‐weighted Interatomic Contact Features Using Extremely Randomized Trees Algorithm

Abstract

The molecular docking simulation is a key computational tool in modern drug discovery research that its predictive performance strongly depends on the employed scoring functions. Many recent studies have shown that the application of machine learning algorithms in the development of scoring functions has led to a significant improvement in docking performance. In this work, we introduce a new machine learning (ML) based scoring function called ET‐Score, which employs the distance‐weighted interatomic contacts between atom type pairs of the ligand and the protein for featurizing protein−ligand complexes and Extremely Randomized Trees algorithm for the training process. The performance of ET‐Score is compared with some successful ML‐based scoring functions and several popular classical scoring functions on the PDBbind 2016v core set. It is shown that our ET‐Score model (with Pearson s correlation of 0.827 and RMSE of 1.332) achieves very good performance in comparison with most of the ML‐based scoring functions and all classical scoring functions despite its extremely low computational cost. ET‐Score s codes are freely available on the web at https://github.com/miladrayka/ET_Score.