ERL-ProLiGraph: Enhanced representation learning on protein-ligand graph structured data for binding affinity prediction.

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Abstract

Predicting Protein-Ligand Binding Affinity (PLBA) is pivotal in drug development, as accurate estimations of PLBA expedite the identification of promising drug candidates for specific targets, thereby accelerating the drug discovery process. Despite substantial advancements in PLBA prediction, developing an efficient and more accurate method remains non-trivial. Unlike previous computer-aid PLBA studies which primarily using ligand SMILES and protein sequences represented as strings, this research introduces a Deep Learning-based method, the Enhanced Representation Learning on Protein-Ligand Graph Structured data for Binding Affinity Prediction (ERL-ProLiGraph). The unique aspect of this method is the use of graph representations for both proteins and ligands, intending to learn structural information continued from both to enhance the accuracy of PLBA predictions. In these graphs, nodes represent atomic structures, while edges depict chemical bonds and spatial relationship. The proposed model, leveraging deep-learning algorithms, effectively learns to correlate these graphical representations with binding affinities. This graph-based representations approach enhances the model’s ability to capture the complex molecular interactions critical in PLBA. This work represents a promising advancement in computational techniques for protein-ligand binding prediction, offering a potential path toward more efficient and accurate predictions in drug development. Comparative analysis indicates that the proposed ERL-ProLiGraph outperforms previous models, showcasing notable efficacy and providing a more suitable approach for accurate PLBA predictions.© 2024 The Author(s). Molecular Informatics published by Wiley-VCH GmbH.