ODesign: A World Model for Biomolecular Interaction Design
Authors: name: Odin Zhang; name: Xujun Zhang; name: Haitao Lin; name: Cheng Tan; name: Qinghan Wang; name: Yuanle Mo; name: Qiantai Feng; name: Gang Du; name: Yuntao Yu; name: Zichang Jin; name: Ziyi You; name: Peicong Lin; name: Yijie Zhang; name: Yuyang Tao; name: Shicheng Chen; name: Jack Xiaoyu Chen; name: Chenqing Hua; name: Weibo Zhao; name: Runze Ma; name: Yunpeng Xia; name: Kejun Ying; name: Jun Li; name: Yundian Zeng; name: Lijun Lang; name: Peichen Pan; name: Hanqun Cao; name: Zihao Song; name: Bo Qiang; name: Jiaqi Wang; name: Pengfei Ji; name: Lei Bai; name: Jian Zhang; name: Chang-yu Hsieh; name: Pheng Ann Heng; name: Siqi Sun; name: Tingjun Hou; name: Shuangjia Zheng
Published: 2025-10-25 14:16:17

Abstract: 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 ,