{"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/structure-based-drug-design-by-denoising","title":"Structure-based drug design by denoising voxel grids","arxiv_id":"2405.03961","date":"2024-05-07","proceeding":null,"authors":["Pedro O. Pinheiro","Arian Jamasb","Omar Mahmood","Vishnu Sresht","Saeed Saremi"],"abstract":"We present VoxBind, a new score-based generative model for 3D molecules conditioned on protein structures. Our approach represents molecules as 3D atomic density grids and leverages a 3D voxel-denoising network for learning and generation. We extend the neural empirical Bayes formalism (Saremi & Hyvarinen, 2019) to the conditional setting and generate structure-conditioned molecules with a two-step procedure: (i) sample noisy molecules from the Gaussian-smoothed conditional distribution with underdamped Langevin MCMC using the learned score function and (ii) estimate clean molecules from the noisy samples with single-step denoising. Compared to the current state of the art, our model is simpler to train, significantly faster to sample from, and achieves better results on extensive in silico benchmarks -- the generated molecules are more diverse, exhibit fewer steric clashes, and bind with higher affinity to protein pockets. The code is available at https://github.com/genentech/voxbind/.","url_abs":"https://arxiv.org/abs/2405.03961v2","url_pdf":"https://arxiv.org/pdf/2405.03961v2.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":"structure-based-drug-design-by-denoising","repo_url":"https://github.com/genentech/voxbind","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"Apache-2.0"}}],"tasks":[{"task_slug":"denoising","task_name":"Denoising"},{"task_slug":"drug-design","task_name":"Drug Design"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2405.03961","atlas_url":"https://app.syntology.ai/?focus=2405.03961","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2405.03961"}},"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. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/genentech/voxbind","reach":{"status":"ok","spdx":"Apache-2.0"}}],"summary":{"ran":7,"unverified":2},"by_repo_kind":{"official":{"samples":9,"ran":7,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"8432abdeb8c89d53","entry":"create_metrics_for_training","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/metrics.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/metrics.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"8432abdeb8c89d53"}},{"code_sha256_prefix":"cb403ae512f88f06","entry":"find_peaks","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/voxelizer.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/voxelizer.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":true,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"cb403ae512f88f06"}},{"code_sha256_prefix":"f721b76027c8f1ae","entry":"get_pocket_mask","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/models/voxbind.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/models/voxbind.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"f721b76027c8f1ae"}},{"code_sha256_prefix":"f261eca8ec467221","entry":"load_checkpoint","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/utils/base_utils.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/utils/base_utils.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"f261eca8ec467221"}},{"code_sha256_prefix":"6df57894ffadaac0","entry":"local_maxima","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/voxelizer.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/voxelizer.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"6df57894ffadaac0"}},{"code_sha256_prefix":"9d58819b8f493f4e","entry":"supress_stdout","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/utils/base_utils.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/utils/base_utils.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"9d58819b8f493f4e"}},{"code_sha256_prefix":"32a8db8324b02b71","entry":"unrotate_voxel_grids","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/models/voxbind.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/models/voxbind.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"32a8db8324b02b71"}},{"code_sha256_prefix":"7ae7b3cd89498518","entry":"get_atom_coords","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/voxelizer.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/voxelizer.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"7ae7b3cd89498518"}},{"code_sha256_prefix":"c5e53403cd6d3069","entry":"rotate_batch_voxel_grids","repo":"genentech/voxbind","repo_kind":"official","path":"voxbind/models/voxbind.py","file_url":"https://github.com/genentech/voxbind/blob/HEAD/voxbind/models/voxbind.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"Apache-2.0","inline_ok":true,"mcp_get_code":{"code_sha256":"c5e53403cd6d3069"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}