{"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/simple-end-to-end-deep-learning-model-for-cdr","title":"Simple End-to-end Deep Learning Model for CDR-H3 Loop Structure Prediction","arxiv_id":"2111.10656","date":"2021-11-20","proceeding":null,"authors":["Natalia Zenkova","Ekaterina Sedykh","Tatiana Shugaeva","Vladislav Strashko","Timofei Ermak","Aleksei Shpilman"],"abstract":"Predicting a structure of an antibody from its sequence is important since it allows for a better design process of synthetic antibodies that play a vital role in the health industry. Most of the structure of an antibody is conservative. The most variable and hard-to-predict part is the third complementarity-determining region of the antibody heavy chain (CDR H3). Lately, deep learning has been employed to solve the task of CDR H3 prediction. However, current state-of-the-art methods are not end-to-end, but rather they output inter-residue distances and orientations to the RosettaAntibody package that uses this additional information alongside statistical and physics-based methods to predict the 3D structure. This does not allow a fast screening process and, therefore, inhibits the development of targeted synthetic antibodies. In this work, we present an end-to-end model to predict CDR H3 loop structure, that performs on par with state-of-the-art methods in terms of accuracy but an order of magnitude faster. We also raise an issue with a commonly used RosettaAntibody benchmark that leads to data leaks, i.e., the presence of identical sequences in the train and test datasets.","url_abs":"https://arxiv.org/abs/2111.10656v2","url_pdf":"https://arxiv.org/pdf/2111.10656v2.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":"simple-end-to-end-deep-learning-model-for-cdr","repo_url":"https://github.com/jbr-ai-labs/simpledh3","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":"https://app.syntology.ai/?focus=2111.10656","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2111.10656"}},"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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