iGNM:: a database of protein functional motions based on Gaussian Network Model
iGNM:: a database of protein functional motions based on Gaussian Network Model
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DOI：
10.1093/bioinformatics/bti469
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发表时间：
2005-07-01
期刊：
影响因子：
5.8
通讯作者：
Bahar, I
中科院分区：
文献类型：
--
作者：
Yang, LW;Liu, X;Bahar, I
动机：蛋白质结构的知识不足以理解和控制其功能。函数是一个动态属性。虽然蛋白质结构信息已迅速积累在数据库中，很少的努力已经投入到系统地表征蛋白质动力学的日期。最近的成功的分析方法的基础上弹性网络模型，特别是高斯网络模型（GNM），使我们能够进行高通量的分析的集体dynamics的protein.Results：我们计算了GNM动态20 058结构蛋白质数据库，并生成信息的平衡动态在单个残基的水平。这些结果储存在一个称为iGNM的网络系统中，其配置允许用户使用简单的搜索引擎通过标准网络浏览器可视化或下载结果。静态和动画图像用于描述蛋白质在广泛的正常模式下的构象迁移率，沿着在线计算引擎可用于新沉积的结构。20个非同源水解酶的动力学的案例研究，以说明的iGNM数据库的效用，确定关键的残基控制的合作运动，并揭示集体动力学和催化活性之间的联系。
Motivation: The knowledge of protein structure is not sufficient for understanding and controlling its function. Function is a dynamic property. Although protein structural information has been rapidly accumulating in databases, little effort has been invested to date toward systematically characterizing protein dynamics. The recent success of analytical methods based on elastic network models, and in particular the Gaussian Network Model (GNM), permits us to perform a high-throughput analysis of the collective dynamics of proteins.Results: We computed the GNM dynamics for 20 058 structures from the Protein Data Bank, and generated information on the equilibrium dynamics at the level of individual residues. The results are stored on a web-based system called iGNM and configured so as to permit the users to visualize or download the results through a standard web browser using a simple search engine. Static and animated images for describing the conformational mobility of proteins over a broad range of normal modes are accessible, along with an online calculation engine available for newly deposited structures. A case study of the dynamics of 20 non-homologous hydrolases is presented to illustrate the utility of the iGNM database for identifying key residues that control the cooperative motions and revealing the connection between collective dynamics and catalytic activity.