ODesign: A World Model for Biomolecular Interaction Design
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arXiv
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| Autori principali: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Natura: | Preprint |
| Pubblicazione: |
2025
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| _version_ | 1866909872866459648 |
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| author | Zhang, Odin Zhang, Xujun Lin, Haitao Tan, Cheng Wang, Qinghan Mo, Yuanle Feng, Qiantai Du, Gang Yu, Yuntao Jin, Zichang You, Ziyi Lin, Peicong Zhang, Yijie Tao, Yuyang Chen, Shicheng Chen, Jack Xiaoyu Hua, Chenqing Zhao, Weibo Ma, Runze Xia, Yunpeng Ying, Kejun Li, Jun Zeng, Yundian Lang, Lijun Pan, Peichen Cao, Hanqun Song, Zihao Qiang, Bo Wang, Jiaqi Ji, Pengfei Bai, Lei Zhang, Jian Hsieh, Chang-yu Heng, Pheng Ann Sun, Siqi Hou, Tingjun Zheng, Shuangjia |
| author_facet | Zhang, Odin Zhang, Xujun Lin, Haitao Tan, Cheng Wang, Qinghan Mo, Yuanle Feng, Qiantai Du, Gang Yu, Yuntao Jin, Zichang You, Ziyi Lin, Peicong Zhang, Yijie Tao, Yuyang Chen, Shicheng Chen, Jack Xiaoyu Hua, Chenqing Zhao, Weibo Ma, Runze Xia, Yunpeng Ying, Kejun Li, Jun Zeng, Yundian Lang, Lijun Pan, Peichen Cao, Hanqun Song, Zihao Qiang, Bo Wang, Jiaqi Ji, Pengfei Bai, Lei Zhang, Jian Hsieh, Chang-yu Heng, Pheng Ann Sun, Siqi Hou, Tingjun Zheng, Shuangjia |
| contents | Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged as powerful tools for molecular design, yet most remain specialized for individual molecular types and lack fine-grained control over interaction details. Here we present ODesign, an all-atom generative world model for all-to-all biomolecular interaction design. ODesign allows scientists to specify epitopes on arbitrary targets and generate diverse classes of binding partners with fine-grained control. Across entity-, token-, and atom-level benchmarks in the protein modality, ODesign demonstrates superior controllability and performance to modality-specific baselines. Extending beyond proteins, it generalizes to nucleic acid and small-molecule design, enabling interaction types such as protein-binding RNA/DNA and RNA/DNA-binding ligands that were previously inaccessible. By unifying multimodal biomolecular interactions within a single generative framework, ODesign moves toward a general-purpose molecular world model capable of programmable design. ODesign is available at https://odesign.lglab.ac.cn , |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2510_22304 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | ODesign: A World Model for Biomolecular Interaction Design Zhang, Odin Zhang, Xujun Lin, Haitao Tan, Cheng Wang, Qinghan Mo, Yuanle Feng, Qiantai Du, Gang Yu, Yuntao Jin, Zichang You, Ziyi Lin, Peicong Zhang, Yijie Tao, Yuyang Chen, Shicheng Chen, Jack Xiaoyu Hua, Chenqing Zhao, Weibo Ma, Runze Xia, Yunpeng Ying, Kejun Li, Jun Zeng, Yundian Lang, Lijun Pan, Peichen Cao, Hanqun Song, Zihao Qiang, Bo Wang, Jiaqi Ji, Pengfei Bai, Lei Zhang, Jian Hsieh, Chang-yu Heng, Pheng Ann Sun, Siqi Hou, Tingjun Zheng, Shuangjia Biomolecules Biomolecular interactions underpin almost all biological processes, and their rational design is central to programming new biological functions. Generative AI models have emerged as powerful tools for molecular design, yet most remain specialized for individual molecular types and lack fine-grained control over interaction details. Here we present ODesign, an all-atom generative world model for all-to-all biomolecular interaction design. ODesign allows scientists to specify epitopes on arbitrary targets and generate diverse classes of binding partners with fine-grained control. Across entity-, token-, and atom-level benchmarks in the protein modality, ODesign demonstrates superior controllability and performance to modality-specific baselines. Extending beyond proteins, it generalizes to nucleic acid and small-molecule design, enabling interaction types such as protein-binding RNA/DNA and RNA/DNA-binding ligands that were previously inaccessible. By unifying multimodal biomolecular interactions within a single generative framework, ODesign moves toward a general-purpose molecular world model capable of programmable design. ODesign is available at https://odesign.lglab.ac.cn , |
| title | ODesign: A World Model for Biomolecular Interaction Design |
| topic | Biomolecules |
| url | https://arxiv.org/abs/2510.22304 |