ElNemo:: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
ElNemo:: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
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DOI：
10.1093/nar/gkh368
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发表时间：
2004-07-01
影响因子：
14.9
通讯作者：
Sanejouand, YH
中科院分区：
文献类型：
--
作者：
Suhre, K;Sanejouand, YH
简正波分析（NMA）是预测给定大分子可能运动的有力工具。最近的研究表明，一半已知的蛋白质运动可以通过使用最多两个低频简正模来建模。NMA的应用涵盖了结构生物学的广泛领域，例如研究配体结合后的蛋白质构象变化、膜通道打开和关闭、核糖体的潜在运动以及病毒衣壳成熟。NMA的另一个新兴领域与通过X射线晶体学确定蛋白质结构有关，其中正常模式扰动模型用作通过分子置换（MR）进行衍射数据定相的模板。在这里，我们介绍了ElNemo，一个弹性网络模型的网络接口，它提供了一个快速简单的工具来计算，可视化和分析大分子的低频正常模式，并生成大量不同的起始模型用于MR。由于ElNemo中实现的“旋转-平移-块”（RTB）近似，可处理的蛋白质的大小实际上没有上限。在蛋白质数据库（PDB）格式的蛋白质结构输入后，ElNemo计算其100个最低频率模式，并产生一组全面的描述性参数和可视化，例如运动的集体性程度，残差均方位移，距离波动图以及观察到的和正常模式衍生的原子位移参数（B因子）之间的相关性。可以生成任意数量的MR简正模扰动模型供下载。如果相同（或同源）蛋白质的两种构象可用，ElNemo识别对相应蛋白质运动贡献最大的正常模式。网站服务器可以在http://igs-server.cnrs-mrs.fr/elnemo/index.html上自由访问。
Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNemo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNemo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNemo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNemo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html.