Anisotropic network model: systematic evaluation and a new web interface
Anisotropic network model: systematic evaluation and a new web interface
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DOI：
10.1093/bioinformatics/btl448
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发表时间：
2006-11-01
期刊：
影响因子：
5.8
通讯作者：
Bahar, Ivet
中科院分区：
文献类型：
--
作者：
Eyal, Eran;Yang, Lee-Wei;Bahar, Ivet
动机：各向异性网络模型（ANM）是一个简单而强大的模型，用于蛋白质的正常模式分析。尽管它广泛用于探索生物分子的集体运动，ANM尚未进行系统的评估。缺乏一个方便的界面一直是一个额外的障碍，易于use.Results：ANM已评估了一个大的蛋白质组，建立最佳的模型参数，实现最高的相关性与实验数据和其准确性和适用性的限制。球状蛋白质中的残留物波动被证明是更准确地预测比那些在nonglobular蛋白质，和核心残留物更准确地描述比溶剂暴露的。与实验一致的显着改善，观察到增加的分辨率的检查结构。提出了一种新的ANM计算服务器，它提供了灵活的选项，用于控制模型参数和输出格式，交互式动画的集体模式和先进的图形功能。
Motivation: The Anisotropic Network Model (ANM) is a simple yet powerful model for normal mode analysis of proteins. Despite its broad use for exploring biomolecular collective motions, ANM has not been systematically evaluated to date. A lack of a convenient interface has been an additional obstacle for easy usage.Results: ANM has been evaluated on a large set of proteins to establish the optimal model parameters that achieve the highest correlation with experimental data and its limits of accuracy and applicability. Residue fluctuations in globular proteins are shown to be more accurately predicted than those in nonglobular proteins, and core residues are more accurately described than solvent-exposed ones. Significant improvement in agreement with experiments is observed with increase in the resolution of the examined structure. A new server for ANM calculations is presented, which offers flexible options for controlling model parameters and output formats, interactive animation of collective modes and advanced graphical features.