{"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/enhancing-ligand-pose-sampling-for-molecular","title":"Enhancing Ligand Pose Sampling for Molecular Docking","arxiv_id":"2312.00191","date":"2023-11-30","proceeding":null,"authors":["Patricia Suriana","Ron O. Dror"],"abstract":"Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must generate a set of candidate ligand binding poses. Unfortunately, the sampling protocols currently used to generate candidate poses frequently fail to produce any poses close to the correct, experimentally determined pose, unless information about the correct pose is provided. This limits the accuracy of learned scoring functions and molecular docking. Here, we describe two improved protocols for pose sampling: GLOW (auGmented sampLing with sOftened vdW potential) and a novel technique named IVES (IteratiVe Ensemble Sampling). Our benchmarking results demonstrate the effectiveness of our methods in improving the likelihood of sampling accurate poses, especially for binding pockets whose shape changes substantially when different ligands bind. This improvement is observed across both experimentally determined and AlphaFold-generated protein structures. Additionally, we present datasets of candidate ligand poses generated using our methods for each of around 5,000 protein-ligand cross-docking pairs, for training and testing scoring functions. To benefit the research community, we provide these cross-docking datasets and an open-source Python implementation of GLOW and IVES at https://github.com/drorlab/GLOW_IVES .","url_abs":"https://arxiv.org/abs/2312.00191v1","url_pdf":"https://arxiv.org/pdf/2312.00191v1.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":"enhancing-ligand-pose-sampling-for-molecular","repo_url":"https://github.com/drorlab/glow_ives","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"none","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"molecular-docking","task_name":"Molecular Docking"},{"task_slug":"pose-prediction","task_name":"Pose Prediction"}],"methods":[{"method_slug":"activation-normalization","method_name":"Activation Normalization"},{"method_slug":"affine-coupling","method_name":"Affine Coupling"},{"method_slug":"glow","method_name":"GLOW"},{"method_slug":"invertible-1x1-convolution","method_name":"Invertible 1x1 Convolution"},{"method_slug":"normalizing-flows","method_name":"Normalizing Flows"},{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2312.00191","atlas_url":"https://app.syntology.ai/?focus=2312.00191","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2312.00191"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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