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使用ROSIE-PARCS网络服务器的投影近似来预测离子移动性碰撞截面.

S M Bargeen Alam Turzo¹, Justin T Seffernick¹, Sergey Lyskov²

¹Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, Ohio State University, Columbus, OH 43210, USA.

Briefings in bioinformatics

|August 23, 2023

概括

我们开发了ROSIE-PARCS,这是一个用户友好的网络工具,用于从结构中预测蛋白质碰撞截面 (CCSIM). 该工具准确估计蛋白质的大小和形状,有助于评估蛋白质结构预测模型,如AlphaFold2.2.

关键词:

在AlphaFold2中,我们使用了AlphaFold2.碰撞的横截面截面是什么离子移动性的离子移动性质谱测量质谱测量质谱测量质谱测量质量测量质谱测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量质量测量蛋白质结构预测蛋白质结构预测网络服务器网络服务器

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科学领域:

结构生物学是结构生物学.
计算化学是一种计算化学.
生物物理学的生物物理.

背景情况:

离子流动性质谱学为蛋白质结构提供了洞察力,特别是碰撞截面 (CCSIM).
现有的CCSIM预测计算方法通常需要命令行专业知识.
使用粗圆形的投影近似 (PARCS) 是用于CCSIM预测的计算方法.

研究的目的:

介绍一个用户友好的网络应用程序,用于从蛋白质结构中预测CCSIM.
为更广泛的科学受众简化PARCS方法的应用.
评估新Web应用程序的准确性及其在评估蛋白质结构预测中的实用性.

主要方法:

开发一个集成到Rosetta Online Server that Includes Everyone (ROSIE) 网络服务器中的Web应用程序.
通过PDB文件输入蛋白质结构到ROSIE-PARCS网络界面.
在Web应用程序中使用PARCS算法进行CCSIM预测.

主要成果:

罗西-帕克斯网络应用程序提供高度准确的CCSIM预测,平均误差为6.12%.
实验CCSIM和预测的CCSPARCS之间的差异可以区分准确的和不准确的AlphaFold2结构预测.
网页界面是公开可访问的,免费使用,并支持所有主要的Web浏览器.

结论:

罗西-帕克斯提供了一种简化和准确的方法来预测蛋白质CCSIM.
该工具提高了研究人员对计算结构分析的可访问性.
ROSIE-PARCS作为验证蛋白质结构模型的宝贵工具,包括来自AlphaFold2.2.的模型.