{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/benchmarking-deep-graph-generative-models-for","title":"Benchmarking Deep Graph Generative Models for Optimizing New Drug Molecules for COVID-19","arxiv_id":"2102.04977","date":"2021-02-09","proceeding":null,"authors":["Logan Ward","Jenna A. Bilbrey","Sutanay Choudhury","Neeraj Kumar","Ganesh Sivaraman"],"abstract":"Design of new drug compounds with target properties is a key area of research in generative modeling. We present a small drug molecule design pipeline based on graph-generative models and a comparison study of two state-of-the-art graph generative models for designing COVID-19 targeted drug candidates: 1) a variational autoencoder-based approach (VAE) that uses prior knowledge of molecules that have been shown to be effective for earlier coronavirus treatments and 2) a deep Q-learning method (DQN) that generates optimized molecules without any proximity constraints. We evaluate the novelty of the automated molecule generation approaches by validating the candidate molecules with drug-protein binding affinity models. The VAE method produced two novel molecules with similar structures to the antiretroviral protease inhibitor Indinavir that show potential binding affinity for the SARS-CoV-2 protein target 3-chymotrypsin-like protease (3CL-protease).","url_abs":"https://arxiv.org/abs/2102.04977v1","url_pdf":"https://arxiv.org/pdf/2102.04977v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"benchmarking-deep-graph-generative-models-for","repo_url":"https://github.com/exalearn/covid-drug-design","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"q-learning","task_name":"Q-Learning"}],"methods":[{"method_slug":"q-learning","method_name":"Q-Learning"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2102.04977","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}