{"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/antibody-antigen-docking-and-design-via","title":"Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement","arxiv_id":"2207.06616","date":"2022-07-14","proceeding":null,"authors":["Wengong Jin","Regina Barzilay","Tommi Jaakkola"],"abstract":"Computational antibody design seeks to automatically create an antibody that binds to an antigen. The binding affinity is governed by the 3D binding interface where antibody residues (paratope) closely interact with antigen residues (epitope). Thus, predicting 3D paratope-epitope complex (docking) is the key to finding the best paratope. In this paper, we propose a new model called Hierarchical Equivariant Refinement Network (HERN) for paratope docking and design. During docking, HERN employs a hierarchical message passing network to predict atomic forces and use them to refine a binding complex in an iterative, equivariant manner. During generation, its autoregressive decoder progressively docks generated paratopes and builds a geometric representation of the binding interface to guide the next residue choice. Our results show that HERN significantly outperforms prior state-of-the-art on paratope docking and design benchmarks.","url_abs":"https://arxiv.org/abs/2207.06616v1","url_pdf":"https://arxiv.org/pdf/2207.06616v1.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":"antibody-antigen-docking-and-design-via","repo_url":"https://github.com/wengong-jin/abdockgen","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"atomic-forces","task_name":"Atomic Forces"},{"task_slug":"decoder","task_name":"Decoder"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2207.06616","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2207.06616"}},"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. 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