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PLMSearch和PLMAlign:基于蛋白语言模型 (PLM) 的同源蛋白序列搜索和对齐

Wei Liu^1,2, Ziye Wang¹, Ronghui You¹

¹Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.

Methods in molecular biology (Clifton, N.J.)

|July 2, 2025

概括

我们开发了PLMSearch和PLMAlign,这两种新的工具使用蛋白质语言模型 (PLM) 来识别和对准与远距离相关的蛋白质序列. 这些方法增强了进化关系推断,超出了传统的序列和结构搜索.

科学领域:

计算生物学是一种计算生物学.
生物信息学是一种生物信息学.
结构生物学是结构生物学.

背景情况:

在计算生物学中,同源蛋白质搜索和序列对齐至关重要.
仅仅从序列中推断遥远的进化关系是具有挑战性的.
现有的结构搜索方法提供了洞察力,但对仅序列分析有局限性.

研究的目的:

介绍基于蛋白质语言模型 (PLM) 的新型工具PLMSearch和PLMAlign.
能够准确识别和对准远程同源蛋白质序列.
使用序列数据推进进化关系的检测.

主要方法:

PLMSearch利用预训练的PLM的深度表示,用于基于序列的同源搜索.
PLMAlign为已识别的同源对提供了准确的序列对齐.
这两种工具都利用实体结构相似性的大型数据集进行培训和验证.

主要成果:

PLMSearch有效地从单独的序列数据中检测远程同质性.
PLMAlign精确地对齐同源蛋白质序列.
提供Web服务器和开源资源,以提供可访问性和进一步研究.

结论:

PLMSearch和PLMAlign代表了蛋白质序列分析的重大进步.
这些基于PLM的工具提高了远程进化关系的检测.
自由可用的资源促进了更广泛的采用和科学发现.

关键词:

同类蛋白质搜索的同类蛋白质搜索大规模的矢量数据库搜索搜索数据库.蛋白质语言模型的模型蛋白质序列对齐是指蛋白质序列对齐.蛋白质结构相似性预测蛋白质结构相似性预测

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