InteracTor: Feature Engineering and Explainable AI for Profiling Protein Structure-Interaction-Function Relationships

Abstract

Characterizing protein families structural and functional diversity is essential for understanding their biological roles. Traditional analyses often focus on primary and secondary structures, which may not fully capture complex protein interactions. Here we introduce InteracTor, a novel toolkit that extracts multimodal features from protein three-dimensional (3D) structures, including interatomic interactions like hydrogen bonds, van der Waals forces, and hydrophobic contacts. By integrating Explainable AI (XAI) techniques, we quantified the importance of the extracted features in the classification of protein structural and functional families. InteracTors interpretable features enable mechanistic insights into the determinants of protein structure, function, and dynamics, offering a transparent means to assess their predictive power within machine learning models. Interatomic interaction features extracted by InteracTor demonstrated superior predictive power for protein family classification compared to features based solely on primary or secondary structure, revealing the importance of considering specific tertiary contacts in computational protein analysis. This work provides a robust framework for future studies aiming to enhance the capabilities of models for protein function prediction and drug discovery. AUTHOR SUMMARYInteracTor is a computational toolkit designed to enhance our understanding of protein structure and function by focusing on three-dimensional (3D) structural interactions. Unlike traditional approaches that primarily rely on sequence or secondary structure data, InteracTor extracts biologically meaningful features such as hydrogen bonds, van der Waals forces, and hydrophobic contacts, which are critical for protein stability and dynamics. By integrating these features into machine learning models alongside explainable AI methods, InteracTor provides interpretable insights into how specific structural interactions influence protein behavior. Our results demonstrate that tertiary structure features significantly improve the accuracy of protein family classification compared to sequence-based methods alone, underscoring the importance of considering 3D interactions in computational protein analyses. The toolkits modular design makes it adaptable for diverse applications, including drug discovery and protein engineering. In a broader context, InteracTor bridges the gap between computational biology and practical applications in medicine and biotechnology by offering a transparent and robust framework for analyzing proteins at a molecular level. This work represents a step forward in leveraging structural data to advance predictive modeling and biological discovery.