ODesign：生物分子相互作用设计的世界模型

摘要

生物分子相互作用支撑着几乎所有生物过程，而其理性设计是编程新生物功能的核心。生成式AI模型已成为分子设计的有力工具，但多数仍专精于单一分子类型，且缺乏对相互作用细节的精细化控制。本文提出ODesign——一个面向全原子全类型生物分子相互作用设计的生成式世界模型。该模型允许科研人员指定任意靶标上的表位，并以精细化控制方式生成多样化的结合配体类别。在蛋白质模态的实体级、令牌级和原子级基准测试中，ODesign展现出优于特定模态基线的可控性与性能。其应用更延伸至蛋白质范畴之外，可泛化至核酸与小分子设计领域，实现了以往难以达成的相互作用类型，如蛋白质结合RNA/DNA、RNA/DNA结合配体等。通过将多模态生物分子相互作用统一于单一生成框架，ODesign朝着构建可编程通用分子世界模型迈出关键一步。该模型已在https://odesign.lglab.ac.cn 开放使用。

English

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 ,

ODesign：生物分子相互作用设计的世界模型

ODesign: A World Model for Biomolecular Interaction Design

摘要

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