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RiboDiffusion:基于三级结构的RNA反折叠与产生性扩散模型

Han Huang^1,2, Ziqian Lin^1,3, Dongchen He¹

¹Department of Computer Science and Engineering, CUHK, Hong Kong SAR, 999077, China.

Bioinformatics (Oxford, England)

|June 28, 2024

概括

RiboDiffusion是一种新的生成模型,从3D结构设计RNA序列,改善合成生物学和治疗学的RNA反折叠. 它在序列恢复和多样性之间提供了平衡,优于现有的方法.

科学领域:

计算生物学计算生物学
合成生物学合成生物学
生物技术是生物技术.

背景情况:

RNA在生物学中的关键作用推动了合成生物学和治疗学的应用.
反向RNA折叠问题,即为特定结构设计功能序列,仍然是一个挑战,特别是在3D构造中.
现有的计算方法主要集中在二次结构上,直接基于3D结构的设计面临数据稀缺性和结构灵活性问题.

研究的目的:

开发一种新的生成模型,RiboDiffusion,用于使用3D结构信息进行RNA逆折叠.
为了使RNA序列的设计符合指定的3D骨干结构.
探索序列恢复和RNA设计中的多样性之间的权衡.

主要方法:

RiboDiffusion采用一种生成扩散模型,集成图形神经网络用于结构和变压器用于序列.
该模型反复地将随机序列改进为受3DRNA骨干结构条件的目标序列.
测试组通过RNA聚类 (序列/结构相似性) 来分层,以评估模型性能.

主要成果:

在序列恢复方面,RiboDiffusion显著优于基线方法,在基于相似性的分割上显示了11-16%的相对改善.
该模型在各种RNA长度和类型中展示了一致的性能.
在形折叠验证证实,生成的序列可以采用目标3DRNA骨干.

结论:

RiboDiffusion为3D结构的RNA逆折叠提供了一种强大的新方法.
该方法有效地导航序列空间,以找到满足结构约束的新型RNA候选者.
这种工具在合成生物学和治疗开发中推进RNA设计方面具有重大潜力.

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