{"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/unimomo-unified-generative-modeling-of-3d","title":"UniMoMo: Unified Generative Modeling of 3D Molecules for De Novo Binder Design","arxiv_id":"2503.19300","date":"2025-03-25","proceeding":null,"authors":["Xiangzhe Kong","Zishen Zhang","Ziting Zhang","Rui Jiao","Jianzhu Ma","Wenbing Huang","Kai Liu","Yang Liu"],"abstract":"The design of target-specific molecules such as small molecules, peptides, and antibodies is vital for biological research and drug discovery. Existing generative methods are restricted to single-domain molecules, failing to address versatile therapeutic needs or utilize cross-domain transferability to enhance model performance. In this paper, we introduce Unified generative Modeling of 3D Molecules (UniMoMo), the first framework capable of designing binders of multiple molecular domains using a single model. In particular, UniMoMo unifies the representations of different molecules as graphs of blocks, where each block corresponds to either a standard amino acid or a molecular fragment. Subsequently, UniMoMo utilizes a geometric latent diffusion model for 3D molecular generation, featuring an iterative full-atom autoencoder to compress blocks into latent space points, followed by an E(3)-equivariant diffusion process. Extensive benchmarks across peptides, antibodies, and small molecules demonstrate the superiority of our unified framework over existing domain-specific models, highlighting the benefits of multi-domain training.","url_abs":"https://arxiv.org/abs/2503.19300v3","url_pdf":"https://arxiv.org/pdf/2503.19300v3.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":"unimomo-unified-generative-modeling-of-3d","repo_url":"https://github.com/kxz18/UniMoMo","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"},{"task_slug":null,"task_name":"Latent Diffusion Model for 3D"}],"methods":[{"method_slug":"diffusion","method_name":"Diffusion"},{"method_slug":"latent-diffusion-model","method_name":"Latent Diffusion Model"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2503.19300","atlas_url":"https://app.syntology.ai/?focus=2503.19300","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2503.19300"}},"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/kxz18/UniMoMo","reach":null}],"summary":{"ran_violates":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"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":"8fb15b5e77827ed9","entry":"to_device","repo":"kxz18/UniMoMo","repo_kind":"official","path":"api/generate.py","file_url":"https://github.com/kxz18/UniMoMo/blob/HEAD/api/generate.py","link_basis":"first_harvest_node","language":"python","status":"ran_violates","verification_level":1,"contract_check":"VIOLATES","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"8fb15b5e77827ed9"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}