arXiv:2603.19473q-bio.BMcs.LG2026-03

用强化学习生成全新且可行的AAV衣壳,突破传统设计局限。

Reinforcement-guided generative protein language models enable de novo design of highly diverse AAV capsids

  • 结合语言模型与强化学习,引导生成高新颖性序列。
  • 生成序列在预测可行性和多样性上均优于传统方法。
  • 适合基因治疗领域研究者和蛋白质设计工程师使用。

腺相关病毒(AAV)载体是基因治疗中广泛使用的递送平台,改进衣壳设计可拓展其治疗潜力。蛋白质设计的核心挑战在于序列空间巨大,而实验筛选规模有限。本文提出基于蛋白质语言模型与强化学习的生成设计框架,通过微调预训练模型学习可行衣壳的模式,并利用联合优化可行性和序列新颖性的奖励函数,引导生成超越训练数据分布的新序列。对比分析显示,仅微调生成的序列虽具高可行性但偏向训练分布,而强化学习引导生成则能探索更远的序列空间,同时保持高可行性。最后,提出融合预测可行性、序列新颖性和生物物理性质的候选筛选策略,用于优先评估。该工作建立了蛋白质序列空间生成探索的通用框架,推动了生成式语言模型在AAV生物工程中的应用。

原文摘要 · Abstract (English)

Adeno-associated viral (AAV) vectors are widely used delivery platforms in gene therapy, and the design of improved capsids is key to expanding their therapeutic potential. A central challenge in AAV bioengineering, as in protein design more broadly, is the vast sequence design space relative to the scale of feasible experimental screening. Machine-guided generative approaches provide a powerful means of navigating this landscape and proposing novel protein sequences that satisfy functional constraints. Here, we develop a generative design framework based on protein language models and reinforcement learning to generate highly novel yet functionally plausible AAV capsids. A pretrained model was fine-tuned on experimentally validated capsid sequences to learn patterns associated with viability. Reinforcement learning was then used to guide sequence generation, with a reward function that jointly promoted predicted viability and sequence novelty, thereby enabling exploration beyond regions represented in the training data. Comparative analyses showed that fine-tuning alone produces sequences with high predicted viability but remains biased toward the training distribution, whereas reinforcement learining-guided generation reaches more distant regions of sequence space while maintaining high predicted viability. Finally, we propose a candidate selection strategy that integrates predicted viability, sequence novelty, and biophysical properties to prioritize variants for downstream evaluation. This work establishes a framework for the generative exploration of protein sequence space and advances the application of generative protein language models to AAV bioengineering.

蛋白质设计生成模型AAV强化学习

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