Transformer neural network for protein-specific drug discovery and validation using QSAR

Amine, Atil Mohamed El; Fadila, Atil

doi:10.1007/s42485-023-00124-6

J Proteins Proteom

2023

DOI: 10.1007/s42485-023-00124-6

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Transformer neural network for protein-specific drug discovery and validation using QSAR

Atil Mohamed El Amine,

Atil Fadila

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2024

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T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction With Uncertainty-Aware Self-Learning for Protein-Specific Alignment

Kyro,

Smaldone,

Shee

et al. 2024

Preprint

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There is significant interest in targeting disease-causing proteins with small molecule inhibitors to restore healthy cellular states. The ability to accurately predict the binding affinity of small molecules to a protein target in silico enables the rapid identification of candidate inhibitors and facilitates the optimization of on-target potency. In this work, we present T-ALPHA, a novel deep learning model that enhances protein-ligand binding affinity prediction by integrating multimodal feature representations within a hierarchical transformer framework to capture information critical to accurately predicting binding affinity. T-ALPHA outperforms all existing models reported in the literature on multiple benchmarks designed to evaluate protein-ligand binding affinity scoring functions. Remarkably, T-ALPHA maintains state-of-the-art performance when utilizing predicted structures rather than crystal structures, a powerful capability in real-world drug discovery applications where experimentally determined structures are often unavailable or incomplete. Additionally, we present an uncertainty-aware self-learning method for protein-specific alignment that does not require additional experimental data, and demonstrate that it improves T-ALPHA’s ability to rank compounds by binding affinity to biologically significant targets such as the SARS-CoV-2 main protease and the epidermal growth factor receptor. To facilitate implementation of T-ALPHA and reproducibility of all results presented in this paper, we have made all of our software available athttps://github.com/gregory-kyro/T-ALPHA.

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T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction With Uncertainty-Aware Self-Learning for Protein-Specific Alignment

Kyro,

Smaldone,

Shee

et al. 2024

Preprint

View full text Add to dashboard Cite

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Transformer neural network for protein-specific drug discovery and validation using QSAR

Cited by 1 publication

References 16 publications

T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction With Uncertainty-Aware Self-Learning for Protein-Specific Alignment

T-ALPHA: A Hierarchical Transformer-Based Deep Neural Network for Protein-Ligand Binding Affinity Prediction With Uncertainty-Aware Self-Learning for Protein-Specific Alignment

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