Advances in Protein-Ligand Binding Affinity Prediction via Deep Learning: A Comprehensive Study of Datasets, Data Preprocessing Techniques, and Model Architectures

Abstract

Background: Drug discovery is a complex and expensive procedure involving several timely and costly phases through which new potential pharmaceutical compounds must pass to get approved. One of these critical steps is the identification and optimization of lead compounds, which has been made more accessible by the introduction of computational methods, including deep learning (DL) techniques. Diverse DL model architectures have been put forward to learn the vast landscape of interaction between proteins and ligands and predict their affinity, helping in the identification of lead compounds. Objective: This survey fills a gap in previous research by comprehensively analyzing the most commonly used datasets and discussing their quality and limitations. It also offers a comprehensive classification of the most recent DL methods in the context of protein-ligand binding affinity prediction, providing a fresh perspective on this evolving field. Methods: We thoroughly examine commonly used datasets for BAP and their inherent characteristics. Our exploration extends to various preprocessing steps and DL techniques, including graph neural networks, convolutional neural networks, and transformers, which are found in the literature. We conducted extensive literature research to ensure that the most recent deep learning approaches for BAP were included by the time of writing this manuscript. Results: The systematic approach used for the present study highlighted inherent challenges to BAP via DL, such as data quality, model interpretability, and explainability, and proposed considerations for future research directions. We present valuable insights to accelerate the development of more effective and reliable DL models for BAP within the research community. Conclusion: The present study can considerably enhance future research on predicting affinity between protein and ligand molecules, hence further improving the overall drug development process.