当前位置: X-MOL 学术Nucleic Acids Res. › 论文详情
Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)
ShiftCrypt: a web server to understand and biophysically align proteins through their NMR chemical shift values.
Nucleic Acids Research ( IF 14.9 ) Pub Date : 2020-05-27 , DOI: 10.1093/nar/gkaa391
Gabriele Orlando 1, 2 , Daniele Raimondi 3 , Luciano Porto Kagami 1 , Wim F Vranken 1, 4, 5
Affiliation  

Nuclear magnetic resonance (NMR) spectroscopy data provides valuable information on the behaviour of proteins in solution. The primary data to determine when studying proteins are the per-atom NMR chemical shifts, which reflect the local environment of atoms and provide insights into amino acid residue dynamics and conformation. Within an amino acid residue, chemical shifts present multi-dimensional and complexly cross-correlated information, making them difficult to analyse. The ShiftCrypt method, based on neural network auto-encoder architecture, compresses the per-amino acid chemical shift information in a single, interpretable, amino acid-type independent value that reflects the biophysical state of a residue. We here present the ShiftCrypt web server, which makes the method readily available. The server accepts chemical shifts input files in the NMR Exchange Format (NEF) or NMR-STAR format, executes ShiftCrypt and visualises the results, which are also accessible via an API. It also enables the ”biophysically-based” pairwise alignment of two proteins based on their ShiftCrypt values. This approach uses Dynamic Time Warping and can optionally include their amino acid code information, and has applications in, for example, the alignment of disordered regions. The server uses a token-based system to ensure the anonymity of the users and results. The web server is available at www.bio2byte.be/shiftcrypt.

中文翻译:

ShiftCrypt:一个Web服务器,通过其NMR化学位移值了解并进行生物物理比对。

核磁共振(NMR)光谱数据提供了有关溶液中蛋白质行为的有价值的信息。确定何时研究蛋白质的主要数据是每原子NMR的化学位移,该位移反映了原子的局部环境,并提供了氨基酸残基动态和构象的见解。在氨基酸残基内,化学位移呈现多维且复杂的互相关信息,使其难以分析。ShiftCrypt方法基于神经网络自动编码器体系结构,将每个氨基酸的化学位移信息压缩为一个单一的,可解释的,与氨基酸类型无关的值,以反映残基的生物物理状态。我们在这里展示了ShiftCrypt Web服务器,它使该方法易于使用。服务器接受NMR交换格式(NEF)或NMR-STAR格式的化学位移输入文件,执行ShiftCrypt并可视化结果,这些结果也可以通过API访问。它还可以基于两个蛋白质的ShiftCrypt值实现“基于生物物理学的”成对比对。该方法使用动态时间规整并且可以可选地包括其氨基酸代码信息,并且可以应用于例如无序区域的比对。服务器使用基于令牌的系统来确保用户和结果的匿名性。Web服务器可从www.bio2byte.be/shiftcrypt获得。它还可以基于两个蛋白质的ShiftCrypt值实现“基于生物物理学的”成对比对。该方法使用动态时间规整并且可以可选地包括其氨基酸代码信息,并且可以应用于例如无序区域的比对。服务器使用基于令牌的系统来确保用户和结果的匿名性。Web服务器可从www.bio2byte.be/shiftcrypt获得。它还可以基于两个蛋白质的ShiftCrypt值实现“基于生物物理学的”成对比对。该方法使用动态时间规整并且可以可选地包括其氨基酸代码信息,并且可以应用于例如无序区域的比对。服务器使用基于令牌的系统来确保用户和结果的匿名性。Web服务器可从www.bio2byte.be/shiftcrypt获得。
更新日期:2020-06-27
down
wechat
bug