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使用AlphaFold 3直接建模DNA和RNA的aptamers:用于预测aptamer结构和aptamer-target相互作用的有希望的工具

Steven Ochoa¹, Valeria Tohver Milam^1,2

¹School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr. NW, Atlanta, Georgia 30332-0245, United States.

ACS synthetic biology

|July 3, 2025

概括

AlphaFold 3对预测aptamer结构,准确建模已知结构,但由于训练数据偏差而面临新型结构的局限性显示出希望. 这种工具推进了用于诊断和治疗的吸管设计.

科学领域:

生物化学生物化学
计算生物学计算生物学
结构生物学结构生物学

背景情况:

亚胺是具有诊断和治疗潜力的核酸配体.
准确的3D结构预测对于aptamer设计至关重要,但仍然具有挑战性.
对非蛋白质结构的有限实验数据阻碍了预测建模.

研究的目的:

为了评估 AlphaFold 3 的准确性,用于预测体结构.
为了比较AlphaFold 3预测与实验确定的体结构.
评估AlphaFold 3在推进in silico aptamer设计方面的潜力.

主要方法:

将AlphaFold 3预测与来自蛋白质数据库 (PDB) 的aptamer结构进行了比较.
评估了PDB中不存在的aptamers的AlphaFold 3预测.
评估预测可靠性和重叠与非PDB体的实验数据.

主要成果:

AlphaFold 3 准确地建模了 PDB 解析的体结构,包括 G 四重复和伪结.
对非PDB体的预测显示了与实验数据的合理重叠,包括G-四重复形状.
AlphaFold 3 正确地识别了一些体蛋白复合体中的结合接口.

结论:

AlphaFold 3显示出对体结构预测的潜力,特别是对于已知的结构.
训练数据偏差限制了AlphaFold 3对代表性不足的核酸结构的准确性.
为了可靠地预测复杂的体结构,需要进一步的细化,但这是朝着人工智能驱动的体设计迈出的一步.

关键词:

蛋白质数据库蛋白质数据库这是一个正统的法典.连接器连接器连接器非正规的非正规的这是一种寡核化物.二级结构预测预测二级结构预测结构结合 - 结构结合

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