WEBnm@: a web application for normal mode analyses of proteins.
WEBnm@: a web application for normal mode analyses of proteins.
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DOI：
10.1186/1471-2105-6-52
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发表时间：
2005-03-11
影响因子：
3
通讯作者：
Reuter, N
中科院分区：
文献类型：
--
作者：
Hollup, SM;Salensminde, G;Reuter, N
正态分析（NMA）已成为研究大分子体系中最慢运动的首选方法。NMA特别适用于大型生物分子组装，如跨膜通道或病毒衣壳。NMA依赖于这样一个假设，即具有最低频率的振动正常模式（也称为软模式）描述了蛋白质中最大的运动，并且是与功能相关的。我们开发了一个基于网络的服务器来执行正常模式的计算和不同类型的分析。服务器从用户以PDB格式提供的结构文件开始，计算正常模式，随后向用户提供一系列自动计算；归一化的平方原子位移，向量场表示和前六个振动模式的动画。每个分析都独立于其他分析执行，并且仅使用web浏览器就可以将结果可视化。不需要额外的插件或软件。对于想用自己喜欢的软件分析结果的用户，也可以下载原始结果。该应用程序可在。我们在这里提出的基本理论，应用架构和其特点的说明，以一个大的跨膜蛋白为例。我们构建了一个高效和模块化的web应用程序，用于蛋白质的正常模式分析。非专业人员可以轻松快速地评估多结构域蛋白质组合的灵活性程度，并表征其结构域的大振幅运动。
Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channels or virus capsids. NMA relies on the hypothesis that the vibrational normal modes having the lowest frequencies (also named soft modes) describe the largest movements in a protein and are the ones that are functionally relevant. We developed a web-based server to perform normal modes calculations and different types of analyses. Starting from a structure file provided by the user in the PDB format, the server calculates the normal modes and subsequently offers the user a series of automated calculations; normalized squared atomic displacements, vector field representation and animation of the first six vibrational modes. Each analysis is performed independently from the others and results can be visualized using only a web browser. No additional plug-in or software is required. For users who would like to analyze the results with their favorite software, raw results can also be downloaded. The application is available on . We present here the underlying theory, the application architecture and an illustration of its features using a large transmembrane protein as an example. We built an efficient and modular web application for normal mode analysis of proteins. Non specialists can easily and rapidly evaluate the degree of flexibility of multi-domain protein assemblies and characterize the large amplitude movements of their domains.
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DOI：
10.1073/pnas.80.12.3696
发表时间：
1983-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
GO, N;NOGUTI, T;NISHIKAWA, T
通讯作者：
NISHIKAWA, T
DOI：
10.1016/s1359-0278(97)00024-2
发表时间：
1997-01-01
期刊：
FOLDING & DESIGN
影响因子：
--
作者：
Bahar, I;Atilgan, AR;Erman, B
通讯作者：
Erman, B
影响因子：
14.9
作者：
Cao, ZW;Xue, Y;Chen, YZ
通讯作者：
Chen, YZ
影响因子：
4.1
作者：
Kalé, L;Skeel, R;Schulten, K
通讯作者：
Schulten, K
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M