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GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction
MOTIVATION: Computational approaches for identifying the protein–ligand binding affinity can greatly facilitate drug discovery and development. At present, many deep learning-based models are proposed to predict the protein–ligand binding affinity and achieve significant performance improvement. How...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10243863/ https://www.ncbi.nlm.nih.gov/pubmed/37225408 http://dx.doi.org/10.1093/bioinformatics/btad340 |
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author | Wang, Kaili Zhou, Renyi Tang, Jing Li, Min |
author_facet | Wang, Kaili Zhou, Renyi Tang, Jing Li, Min |
author_sort | Wang, Kaili |
collection | PubMed |
description | MOTIVATION: Computational approaches for identifying the protein–ligand binding affinity can greatly facilitate drug discovery and development. At present, many deep learning-based models are proposed to predict the protein–ligand binding affinity and achieve significant performance improvement. However, protein–ligand binding affinity prediction still has fundamental challenges. One challenge is that the mutual information between proteins and ligands is hard to capture. Another challenge is how to find and highlight the important atoms of the ligands and residues of the proteins. RESULTS: To solve these limitations, we develop a novel graph neural network strategy with the Vina distance optimization terms (GraphscoreDTA) for predicting protein–ligand binding affinity, which takes the combination of graph neural network, bitransport information mechanism and physics-based distance terms into account for the first time. Unlike other methods, GraphscoreDTA can not only effectively capture the protein–ligand pairs’ mutual information but also highlight the important atoms of the ligands and residues of the proteins. The results show that GraphscoreDTA significantly outperforms existing methods on multiple test sets. Furthermore, the tests of drug–target selectivity on the cyclin-dependent kinase and the homologous protein families demonstrate that GraphscoreDTA is a reliable tool for protein–ligand binding affinity prediction. AVAILABILITY AND IMPLEMENTATION: The resource codes are available at https://github.com/CSUBioGroup/GraphscoreDTA. |
format | Online Article Text |
id | pubmed-10243863 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-102438632023-06-07 GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction Wang, Kaili Zhou, Renyi Tang, Jing Li, Min Bioinformatics Original Paper MOTIVATION: Computational approaches for identifying the protein–ligand binding affinity can greatly facilitate drug discovery and development. At present, many deep learning-based models are proposed to predict the protein–ligand binding affinity and achieve significant performance improvement. However, protein–ligand binding affinity prediction still has fundamental challenges. One challenge is that the mutual information between proteins and ligands is hard to capture. Another challenge is how to find and highlight the important atoms of the ligands and residues of the proteins. RESULTS: To solve these limitations, we develop a novel graph neural network strategy with the Vina distance optimization terms (GraphscoreDTA) for predicting protein–ligand binding affinity, which takes the combination of graph neural network, bitransport information mechanism and physics-based distance terms into account for the first time. Unlike other methods, GraphscoreDTA can not only effectively capture the protein–ligand pairs’ mutual information but also highlight the important atoms of the ligands and residues of the proteins. The results show that GraphscoreDTA significantly outperforms existing methods on multiple test sets. Furthermore, the tests of drug–target selectivity on the cyclin-dependent kinase and the homologous protein families demonstrate that GraphscoreDTA is a reliable tool for protein–ligand binding affinity prediction. AVAILABILITY AND IMPLEMENTATION: The resource codes are available at https://github.com/CSUBioGroup/GraphscoreDTA. Oxford University Press 2023-05-24 /pmc/articles/PMC10243863/ /pubmed/37225408 http://dx.doi.org/10.1093/bioinformatics/btad340 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Paper Wang, Kaili Zhou, Renyi Tang, Jing Li, Min GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction |
title | GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction |
title_full | GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction |
title_fullStr | GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction |
title_full_unstemmed | GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction |
title_short | GraphscoreDTA: optimized graph neural network for protein–ligand binding affinity prediction |
title_sort | graphscoredta: optimized graph neural network for protein–ligand binding affinity prediction |
topic | Original Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10243863/ https://www.ncbi.nlm.nih.gov/pubmed/37225408 http://dx.doi.org/10.1093/bioinformatics/btad340 |
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