arXiv:2504.16479q-bio.BMcs.AI2025-04被引 1

用扩散模型从头设计新蛋白质,成功率远超传统方法。

The Dance of Atoms-De Novo Protein Design with Diffusion Model

  • 基于扩散模型生成蛋白质骨架与序列,跳过碎片拼接
  • 在25个任务中成功率达显著高于传统方法
  • 适合蛋白质工程与药物研发人员快速探索新蛋白

从头设计蛋白质指创造自然界不存在但具有特定结构和功能的蛋白质。近年来,高质量蛋白结构与序列数据的积累及技术进步,推动生成式人工智能(AI)模型在蛋白质设计中的成功应用。这些模型超越了依赖片段和生物信息学的传统方法,显著提升了设计成功率并降低实验成本,带来领域突破。在各类生成式AI模型中,扩散模型表现最为突出。过去两到三年间,已有十余款基于扩散模型的蛋白质设计模型出现,其中代表性模型RFDiffusion在25项蛋白质设计任务中表现远超传统方法,其他如RFjoint与hallucination等也取得进展。本文系统回顾扩散模型在生成蛋白质骨架与序列中的应用,分析各模型优缺点,总结成功案例,并探讨未来发展方向。

原文摘要 · Abstract (English)

The de novo design of proteins refers to creating proteins with specific structures and functions that do not naturally exist. In recent years, the accumulation of high-quality protein structure and sequence data and technological advancements have paved the way for the successful application of generative artificial intelligence (AI) models in protein design. These models have surpassed traditional approaches that rely on fragments and bioinformatics. They have significantly enhanced the success rate of de novo protein design, and reduced experimental costs, leading to breakthroughs in the field. Among various generative AI models, diffusion models have yielded the most promising results in protein design. In the past two to three years, more than ten protein design models based on diffusion models have emerged. Among them, the representative model, RFDiffusion, has demonstrated success rates in 25 protein design tasks that far exceed those of traditional methods, and other AI-based approaches like RFjoint and hallucination. This review will systematically examine the application of diffusion models in generating protein backbones and sequences. We will explore the strengths and limitations of different models, summarize successful cases of protein design using diffusion models, and discuss future development directions.

蛋白质设计扩散模型生成AI

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