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