快速而准确的全基因组预测和蛋白质-蛋白质相互作用的结构建模使用银河系
Aysam Guerler1, Dannon Baker2, Marius van den Beek3
1Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA. aysam.guerler@gmail.com.
BMC bioinformatics
|June 23, 2023
概括
我们开发了一种自动化的管道来预测全基因组的蛋白质-蛋白质相互作用,并建模它们的结构. 该工具有助于理解细胞过程并识别药物点,包括与SARS-CoV-2相关的药物点.
科学领域:
- 计算生物学 计算生物学
- 结构生物学 结构生物学
- 生物信息学是一种生物信息学.
背景情况:
- 蛋白质与蛋白质之间的相互作用对细胞功能至关重要.
- 识别这些相互作用为生物系统和潜在的治疗点提供了洞察力.
- 绘制蛋白相互作用的现有方法可能是有限的.
研究的目的:
- 介绍一种新的,自动化的管道,用于预测全基因组的蛋白质与蛋白质相互作用 (PPI).
- 为预测蛋白质复合体生成高质量的多重体结构模型.
- 为研究人员提供公开可访问的工具.
主要方法:
- 开发一个用于PPI预测的自动计算管道.
- 管道的应用到人类和酵母基因组.
- 为已识别的蛋白质复合体生成结构模型.
主要成果:
- 该管道成功预测了人类和酵母基因组中的蛋白质-蛋白质相互作用网络,其质量与实验方法相当.
- 确定并建模了人类蛋白质与SARS-CoV-2帕帕因类蛋白酶 (PLpro) 的相互作用.
- 为与人类受体相互作用的SARS-CoV-2尖端蛋白 (S) 生成结构模型 (髓-基细胞糖蛋白和二基酸酶-4).
结论:
- 开发的方法可靠地识别蛋白质相互作用,并产生高质量的结构模型用于验证.
- 交互原子建模管道在usegalaxy.org和usegalaxy.eu.eu上公开提供.
- 这种工具有助于研究复杂的生物系统,并有助于药物发现.
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