Ligand Binding Prediction using Protein Structure Graphs and Residual Graph Attention Networks [article]

Mohit Pandey, Mariia Radaeva, Hazem Mslati, Olivia Garland, Michael Fernandez, Martin Ester, Artem Cherkasov
<span title="2022-04-28">2022</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
AbstractMotivationComputational prediction of ligand-target interactions is a crucial part of modern drug discovery as it helps to bypass high costs and labor demands of in vitro and in vivo screening. As the wealth of bioactivity data accumulates, it provides opportunities for the development of deep learning (DL) models with increasing predictive powers. Conventionally, such models were either limited to the use of very simplified representations of proteins or ineffective voxelization of
more &raquo; ... r 3D structures. Herein, we present the development of the PSG-BAR (Protein Structure Graph –Binding Affinity Regression) approach that utilizes 3D structural information of the proteins along with 2D graph representations of ligands. The method also introduces attention scores to selectively weight protein regions that are most important for ligand binding.ResultsThe developed approach demonstrates the state-of-the-art performance on several binding affinity benchmarking datasets. The attention-based pooling of protein graphs enables identification of surface residues as critical residues for protein-ligand binding. Finally, we validate our model predictions against an experimental assay on a viral main protease (Mpro)– the hallmark target of SARS-CoV-2 coronavirus.AvailabilityThe code for PSG-BAR is made available at https://github.com/diamondspark/PSG-BARContactacherkasov@prostatecentre.com
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.04.27.489750">doi:10.1101/2022.04.27.489750</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2d5dhwxzlrc6totpqv76tprwuu">fatcat:2d5dhwxzlrc6totpqv76tprwuu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220501025527/https://www.biorxiv.org/content/biorxiv/early/2022/04/28/2022.04.27.489750.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d8/6d/d86d642b0a57544f8be380ea9d59bbc156a91ca9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.04.27.489750"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>