{"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/pocketvina-enables-scalable-and-highly","title":"PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning","arxiv_id":"2506.20043","date":"2025-06-24","proceeding":null,"authors":["Ahmet Sarigun","Bora Uyar","Vedran Franke","Altuna Akalin"],"abstract":"Sampling physically valid ligand-binding poses remains a major challenge in molecular docking, particularly for unseen or structurally diverse targets. We introduce PocketVina, a fast and memory-efficient, search-based docking framework that combines pocket prediction with systematic multi-pocket exploration. We evaluate PocketVina across four established benchmarks--PDBbind2020 (timesplit and unseen), DockGen, Astex, and PoseBusters--and observe consistently strong performance in sampling physically valid docking poses. PocketVina achieves state-of-the-art performance when jointly considering ligand RMSD and physical validity (PB-valid), while remaining competitive with deep learning-based approaches in terms of RMSD alone, particularly on structurally diverse and previously unseen targets. PocketVina also maintains state-of-the-art physically valid docking accuracy across ligands with varying degrees of flexibility. We further introduce TargetDock-AI, a benchmarking dataset we curated, consisting of over 500000 protein-ligand pairs, and a partition of the dataset labeled with PubChem activity annotations. On this large-scale dataset, PocketVina successfully discriminates active from inactive targets, outperforming a deep learning baseline while requiring significantly less GPU memory and runtime. PocketVina offers a robust and scalable docking strategy that requires no task-specific training and runs efficiently on standard GPUs, making it well-suited for high-throughput virtual screening and structure-based drug discovery.","url_abs":"https://arxiv.org/abs/2506.20043v1","url_pdf":"https://arxiv.org/pdf/2506.20043v1.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":"pocketvina-enables-scalable-and-highly","repo_url":"https://github.com/bimsbbioinfo/pocketvina","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":null,"task_name":"GPU"},{"task_slug":"molecular-docking","task_name":"Molecular Docking"},{"task_slug":null,"task_name":"valid"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}