{"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/proteina-scaling-flow-based-protein-structure","title":"Proteina: Scaling Flow-based Protein Structure Generative Models","arxiv_id":"2503.00710","date":"2025-03-02","proceeding":null,"authors":["Tomas Geffner","Kieran Didi","Zuobai Zhang","Danny Reidenbach","Zhonglin Cao","Jason Yim","Mario Geiger","Christian Dallago","Emine Kucukbenli","Arash Vahdat","Karsten Kreis"],"abstract":"Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop Proteina, a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture with up to 5x as many parameters as previous models. To meaningfully quantify performance, we introduce a new set of metrics that directly measure the distributional similarity of generated proteins with reference sets, complementing existing metrics. We further explore scaling training data to millions of synthetic protein structures and explore improved training and sampling recipes adapted to protein backbone generation. This includes fine-tuning strategies like LoRA for protein backbones, new guidance methods like classifier-free guidance and autoguidance for protein backbones, and new adjusted training objectives. Proteina achieves state-of-the-art performance on de novo protein backbone design and produces diverse and designable proteins at unprecedented length, up to 800 residues. The hierarchical conditioning offers novel control, enabling high-level secondary-structure guidance as well as low-level fold-specific generation.","url_abs":"https://arxiv.org/abs/2503.00710v1","url_pdf":"https://arxiv.org/pdf/2503.00710v1.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":"proteina-scaling-flow-based-protein-structure","repo_url":"https://github.com/NVIDIA-Digital-Bio/proteina","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"jax","reach":{"status":"ok","spdx":"NOASSERTION"}}],"tasks":[{"task_slug":"protein-design","task_name":"Protein Design"}],"methods":[{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2503.00710","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2503.00710"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+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/NVIDIA-Digital-Bio/proteina","reach":{"status":"ok","spdx":"NOASSERTION"}}],"summary":{"ran_draft_wrong":1},"by_repo_kind":{},"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":1,"samples":[{"code_sha256_prefix":"fd5db15443a969ae","entry":"create_pad_feats","repo":null,"repo_kind":null,"path":null,"file_url":null,"link_basis":"identical_code_first_harvested_elsewhere","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":true,"licence":null,"inline_ok":false,"mcp_get_code":{"code_sha256":"fd5db15443a969ae"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}