{"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/protein-complex-invariant-embedding-with","title":"Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designer","arxiv_id":"2305.09480","date":"2023-04-21","proceeding":null,"authors":["Cheng Tan","Zhangyang Gao","Lirong Wu","Jun Xia","Jiangbin Zheng","Xihong Yang","Yue Liu","Bozhen Hu","Stan Z. Li"],"abstract":"Antibodies are crucial proteins produced by the immune system in response to foreign substances or antigens. The specificity of an antibody is determined by its complementarity-determining regions (CDRs), which are located in the variable domains of the antibody chains and form the antigen-binding site. Previous studies have utilized complex techniques to generate CDRs, but they suffer from inadequate geometric modeling. Moreover, the common iterative refinement strategies lead to an inefficient inference. In this paper, we propose a \\textit{simple yet effective} model that can co-design 1D sequences and 3D structures of CDRs in a one-shot manner. To achieve this, we decouple the antibody CDR design problem into two stages: (i) geometric modeling of protein complex structures and (ii) sequence-structure co-learning. We develop a novel macromolecular structure invariant embedding, typically for protein complexes, that captures both intra- and inter-component interactions among the backbone atoms, including C$\\alpha$, N, C, and O atoms, to achieve comprehensive geometric modeling. Then, we introduce a simple cross-gate MLP for sequence-structure co-learning, allowing sequence and structure representations to implicitly refine each other. This enables our model to design desired sequences and structures in a one-shot manner. Extensive experiments are conducted to evaluate our results at both the sequence and structure levels, which demonstrate that our model achieves superior performance compared to the state-of-the-art antibody CDR design methods.","url_abs":"https://arxiv.org/abs/2305.09480v5","url_pdf":"https://arxiv.org/pdf/2305.09480v5.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":"protein-complex-invariant-embedding-with","repo_url":"https://github.com/A4Bio/ADesigner","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"specificity","task_name":"Specificity"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2305.09480","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2305.09480"}},"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/A4Bio/ADesigner","reach":null}],"summary":{"ran_fixture":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":1,"samples":[{"code_sha256_prefix":"78febf922c1f462e","entry":"diff_l1_loss","repo":"A4Bio/ADesigner","repo_kind":"official","path":"models/adesigner.py","file_url":"https://github.com/A4Bio/ADesigner/blob/HEAD/models/adesigner.py","link_basis":"first_harvest_node","language":"python","status":"ran_fixture","verification_level":1,"contract_check":"RAISES","metamorphic_tier":"invariant","behaviour_fingerprint":true,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"78febf922c1f462e"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}