3Drefine: an interactive web server for efficient protein structure refinement.
3Drefine: an interactive web server for efficient protein structure refinement.
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DOI：
10.1093/nar/gkw336
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Cheng J
中科院分区：
文献类型：
--
作者：
Bhattacharya D;Nowotny J;Cao R;Cheng J
3Drefine 是一款交互式网络服务器，可实现一致且计算高效的蛋白质结构细化，并能够执行基于网络的统计和可视化分析。 3Drefine 细化协议利用氢键网络的迭代优化与优化模型上的原子级能量最小化相结合，使用复合物理和基于知识的力场来实现高效的蛋白质结构细化。该方法已在盲 CASP 实验以及大规模和多样化的基准数据集上进行了广泛的评估，并且在全局和局部结构质量测量方面均表现出对初始结构的持续改进。 3Drefine 网络服务器允许通过文本或文件输入提交、电子邮件通知、提供的示例提交来方便地精炼蛋白质结构，并且可以免费使用，无需任何注册要求。该服务器还通过配备众多蛋白质模型分析工具的 JSmol 小程序，通过各种能量和统计反馈以及多个精细模型的交互式可视化来提供对提交的综合分析。 Web 服务器已被许多用户广泛测试和使用。因此，3Drefine Web 服务器方便地为社区提供了一个易于访问的有用工具。 3Drefine Web 服务器已在 URL 上公开：http://sysbio.rnet.missouri.edu/3Drefine/。
3Drefine is an interactive web server for consistent and computationally efficient protein structure refinement with the capability to perform web-based statistical and visual analysis. The 3Drefine refinement protocol utilizes iterative optimization of hydrogen bonding network combined with atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields for efficient protein structure refinement. The method has been extensively evaluated on blind CASP experiments as well as on large-scale and diverse benchmark datasets and exhibits consistent improvement over the initial structure in both global and local structural quality measures. The 3Drefine web server allows for convenient protein structure refinement through a text or file input submission, email notification, provided example submission and is freely available without any registration requirement. The server also provides comprehensive analysis of submissions through various energy and statistical feedback and interactive visualization of multiple refined models through the JSmol applet that is equipped with numerous protein model analysis tools. The web server has been extensively tested and used by many users. As a result, the 3Drefine web server conveniently provides a useful tool easily accessible to the community. The 3Drefine web server has been made publicly available at the URL: http://sysbio.rnet.missouri.edu/3Drefine/.