iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.
iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.
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DOI：
10.1093/nar/gkv1236
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发表时间：
2016-01-04
影响因子：
14.9
通讯作者：
Bahar I
中科院分区：
文献类型：
--
作者：
Li H;Chang YY;Yang LW;Bahar I
高斯网络模型（GNM）是研究蛋白质及其复合物动力学的一个简单而强大的模型。GNM分析成为一种广泛使用的方法，用于评估生物分子结构的构象动力学与用户友好的界面和数据库，iGNM，在2005年的发展。我们在这里提出了一个更新的版本，iGNM 2.0 http：//gnmdb.csb.pitt.edu/，它涵盖了超过95%的结构，目前可在蛋白质数据库（PDB）。先进的搜索和可视化功能，包括2D和3D，允许用户检索关于残基间和域间互相关、运动的合作模式、铰链位点的位置和能量定位点的信息。iGNM 2.0能够提供大多数PDB结构的结构动力学数据，特别是其生物组装的数据，这使其成为在结构、动力学和功能之间建立桥梁的有用资源。
Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.