{"id":26098073,"url":"https://github.com/deepbiolab/nano-abnovo","last_synced_at":"2026-03-07T21:03:19.726Z","repository":{"id":280654621,"uuid":"942718992","full_name":"deepbiolab/nano-abnovo","owner":"deepbiolab","description":"Reproducing the core concepts from the paper \"AbNovo: Constrained Preference Optimization for Multi-objective Antibody Design\"","archived":false,"fork":false,"pushed_at":"2025-03-04T15:13:57.000Z","size":4,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-03-04T16:26:50.757Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/deepbiolab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2025-03-04T15:05:24.000Z","updated_at":"2025-03-04T15:14:00.000Z","dependencies_parsed_at":"2025-03-04T16:26:52.661Z","dependency_job_id":"8fd30663-0c03-4302-8f06-ab1a6e477990","html_url":"https://github.com/deepbiolab/nano-abnovo","commit_stats":null,"previous_names":["deepbiolab/nano-abnovo"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/deepbiolab/nano-abnovo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/deepbiolab%2Fnano-abnovo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/deepbiolab%2Fnano-abnovo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/deepbiolab%2Fnano-abnovo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/deepbiolab%2Fnano-abnovo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/deepbiolab","download_url":"https://codeload.github.com/deepbiolab/nano-abnovo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/deepbiolab%2Fnano-abnovo/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30231490,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-07T19:01:10.287Z","status":"ssl_error","status_checked_at":"2026-03-07T18:59:58.103Z","response_time":53,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-09T16:00:00.980Z","updated_at":"2026-03-07T21:03:19.708Z","avatar_url":"https://github.com/deepbiolab.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# **Nano-AbNovo: Constrained Preference Optimization for Antibody Design**\n\n**Nano-AbNovo** is a lightweight and educational version for reproducing the core concepts from the paper *\"AbNovo: Constrained Preference Optimization for Multi-objective Antibody Design\"*. This project implements a diffusion-based model for antibody design, combined with constrained preference optimization (CPO) to meet multi-objective biophysical property requirements.\n\n\n## **Features**\n- **Antibody Design with Diffusion Models**: Joint design of antibody structures and sequences using diffusion generative models.\n- **Constrained Preference Optimization (CPO)**: Optimizes binding affinity while explicitly constraining key biophysical properties such as non-specific binding, self-association, and stability.\n- **Primal-Dual Optimization**: Dynamically adjusts reward and constraint weights to improve training stability.\n- **Structure-aware Protein Language Model**: Leverages large-scale protein structural data to mitigate overfitting caused by limited antibody-antigen training data.\n- **Reproducible Results**: Includes code and configurations to reproduce the main experiments from the paper.\n\n\u003e *Working in progress....*\n\n## **Citations**\n\n```\n@inproceedings{\nren2025multiobjective,\ntitle={Multi-objective antibody design with constrained preference optimization},\nauthor={Milong Ren and ZaiKai He and Haicang Zhang},\nbooktitle={The Thirteenth International Conference on Learning Representations},\nyear={2025},\nurl={https://openreview.net/forum?id=4ktJJBvvUd}\n}\n```\n\n## **Acknowledgements**\nThis project is inspired by the following works:\n- [AbNovo: Multi-objective antibody design with constrained preference optimization](https://openreview.net/forum?id=4ktJJBvvUd)\n- [DiffAb: Denoising Diffusion for Antibody Design](https://www.biorxiv.org/content/10.1101/2022.07.10.499510v5.full.pdf)\n- [AbX: Score-based Diffusion for Antibody Design](https://openreview.net/pdf?id=1YsQI04KaN)\n- [ABDPO: Direct Preference Optimization for Antibody Binding](https://arxiv.org/html/2403.16576v1)\n\n\n## **License**\nThis project is licensed under the MIT License.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdeepbiolab%2Fnano-abnovo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdeepbiolab%2Fnano-abnovo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdeepbiolab%2Fnano-abnovo/lists"}