Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues

Abstract

Predicting interactions between proteins is fundamental for understanding the mechanisms underlying cellular processes, since protein–protein complexes are crucial in physiological conditions but also in many diseases, for example by seeding aggregates formation. Despite the many advancements made so far, the performance of docking protocols is deeply dependent on their capability to identify binding regions. From this, the importance of developing low-cost and computationally efficient methods in this field. We present an integrated novel protocol mainly based on compact modeling of protein surface patches via sets of orthogonal polynomials to identify regions of high shape/electrostatic complementarity. By incorporating both hydrophilic and hydrophobic contributions, we define new binding matrices, which serve as effective inputs for training a neural network. In this work, we propose a new Neural Network (NN)-based architecture, Core Interacting Residues Network (CIRNet), which achieves a performance in terms of Area Under the Receiver Operating Characteristic Curve (ROC AUC) of approximately 0.87 in identifying pairs of core interacting residues on a balanced data set. In a blind search for core interacting residues, CIRNet distinguishes them from random decoys with an ROC AUC of 0.72. We test this protocol to enhance docking algorithms by filtering the proposed poses, addressing one of the still open problems in computational biology. Notably, when applied to the top ten models from three widely used docking servers, CIRNet improves docking outcomes, significantly reducing the average RMSD between the selected poses and the native state. Compared to another state-of-the-art tool for rescaling docking poses, CIRNet more efficiently identified the worst poses generated by the three docking servers under consideration and achieved superior rescaling performance in two cases.