A-CODE首次实现原子级统一蛋白质共设计，效率与精度双突破。
A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion
- 基于原子级扩散模型，一步完成氨基酸类型与坐标联合优化。
- 在绑定蛋白设计中，硬任务成功率提升十倍，逼近顶尖两阶段模型水平。
- 天然支持非标准氨基酸建模，可拓展至复杂生物分子系统。
我们提出A-CODE，一种全原子级的统一单阶段蛋白质共设计模型，同时优化离散的原子类型与连续的原子坐标。不同于主流的两阶段方法（先结构设计再序列设计），A-CODE在统一的多模态扩散框架内实现完全原子级建模，残基身份仅由原子级预测推导得出。基于强大的全原子架构，A-CODE在无条件蛋白质生成任务中表现卓越，优于所有现有单阶段与两阶段设计模型。在结合物设计方面，A-CODE的表现媲美甚至超越现有最先进两阶段模型，并相较已有单阶段共设计模型，在困难任务上成功率达到十倍提升。其内在的原子形式灵活性首次实现了对非标准氨基酸（ncAA）建模的无缝适配。本全原子框架为全原子生成建模建立了全新且通用的基础，可自然扩展至复杂生物分子体系。
原文摘要 · Abstract (English)
We present A-CODE, a fully atomic unified one-stage protein co-design model that simultaneously refines discrete atom types and continuous atom coordinates. Unlike predominant two-stage methods that cascade structure design with amino acid-level sequence design, our approach is fully atomic within a unified multimodal diffusion framework, in which residue identities are inferred solely from atom-level predictions. Built upon the powerful all-atom architecture, A-CODE achieves superior designability for unconditional protein generation, outperforming all existing one-stage and two-stage design models. For binder design, A-CODE rivals and even outperforms existing state-of-the-art two-stage design models and, compared with the existing one-stage co-design model, achieves a drastic tenfold improvement in success rate on hard tasks. The inherent flexibility of our atomic formulation enables, for the first time, seamless adaptation to non-canonical amino acid (ncAA) modeling. Our fully atomic framework establishes a new, versatile foundation for all-atom generative modeling that can be naturally extended to complex biomolecular systems.
Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品；中文卡片由大模型生成，请以原文为准。