PTM-Mamba:一种 PTM 意识的蛋白质语言模型,具有双向封闭的 Mamba 块
Fred Zhangzhi Peng1, Chentong Wang2, Tong Chen1
1Department of Biomedical Engineering, Duke University, Durham, NC, USA.
Nature methods
|April 10, 2025
概括
我们介绍了PTM-Mamba,这是一个新的蛋白质语言模型,包含了翻译后修改 (PTM). 这一进步使得对各种应用的蛋白质多样性,功能和相互作用能够进行更准确的建模.
科学领域:
- 蛋白质组学是指蛋白质组学.
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 当前的蛋白质语言模型 (LMs) 擅长编码蛋白质特性,但缺乏对翻译后修改 (PTMs) 的表示.
- PTM对蛋白质组的多样性至关重要,影响蛋白质的结构,功能和相互作用.
- 现有的模型不能完全捕捉到由PTMs引入的复杂性.
研究的目的:
- 开发一个PTM意识的蛋白质语言模型,整合PTM信息.
- 为了能够准确地建模野生类型和PTM修改的蛋白质序列.
- 建立一个基础工具,用于PTM意识的蛋白质建模和设计.
主要方法:
- 开发了PTM-Mamba,一种新的蛋白质LM架构.
- 使用双向Mamba块集成的PTM代币.
- 通过一种新的门锁机制,与ESM-2蛋白质LM嵌入的PTM代币融合.
主要成果:
- PTM-Mamba独特地模拟了野生类型和PTM序列.
- 启用下游任务,包括疾病关联和药物可用性预测.
- 便于预测PTM对蛋白质-蛋白质相互作用的影响以及零射击PTM的发现.
结论:
- 在蛋白质语言建模方面,PTM-Mamba代表了显著的进步.
- 该模型为了解PTMs在蛋白质功能中的作用提供了一个强大的工具.
- 建立了PTM-Mamba作为PTM意识的蛋白质研究和设计的基础资源.
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