3bmGPT: A novel language model for transforming and analyzing protein-ligand binding interactions in drug discovery.

3bmGPT: A novel language model for transforming and analyzing protein-ligand binding interactions in drug discovery. | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article 3bmGPT: A novel language model for transforming and analyzing protein-ligand binding interactions in drug discovery. Jongsun Jung, Taeseob Lee, Jonathan Witztum, Heehoon Jung, Ahnjae Jung, and 5 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3760296/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Emergent Large Language Models (LLMs) show impressive capabilities in performing a wide range of tasks. These models can be harnessed for biophysical use, as well. The main challenge in this endeavor lies in transforming 3D chemical data into 1D language-like data. We developed a method to transform molecular data into language-like data and tokenize it for LLM use in biophysical context. We then trained a model, 3bmGPT, and validated it with a known protein-ligand complex. Using the pre-trained result, the model can assess the chemical properties of targets, detect shared binding properties and structures, and reveal related drugs. 3bmGPT and the synthetic-language to describe binding interactions uncovered novel protein-protein networks influenced by ligands, indicating functionally related yet previously unreported interactions. We provide open access to a fully functional web-based tool utilizing 3bmGPT. Biological sciences/Computational biology and bioinformatics/Machine learning Biological sciences/Drug discovery Biological sciences/Computational biology and bioinformatics/Computational models Full Text Additional Declarations Yes there is potential Competing Interest. T.L., J.W., H.J., A.J., J.M., J.H.H., and J.J. have a financial interest in Syntekabio Incorporated, a biotechnology company focused on the drug development using AI algorithms. J.W. and J.J. have a financial interest in Syntekabio USA Incorporated, a business subsidiary of Syntekabio Incorporated. C.Z. has a financial interest in Cerebras Systems, an AI company building computer systems for AI applications. Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. 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