GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data.
GUARDD: user-friendly MATLAB software for rigorous analysis of CPMG RD NMR data.
复制标题
DOI：
10.1007/s10858-011-9589-y
复制
发表时间：
2012-01
影响因子：
2.7
通讯作者：
Foster MP
中科院分区：
文献类型：
--
作者：
Kleckner IR;Foster MP
分子动力学对于生命是必不可少的，自20世纪50年代以来，核磁共振（NMR）光谱已被广泛用于表征这些现象。在过去的15年里，Carr-Purcell Meiboom-Gill弛豫色散（CPMG RD）NMR实验为先进的NMR实验室提供了在关键的μs-ms时间窗口内获得蛋白质和RNA动力学的动力学，热力学和结构细节的机会。然而，RD数据的分析具有挑战性，因为数据集通常很大，需要许多非线性拟合参数，从而混淆准确性评估。此外，新手CPMG实验者面临着额外的障碍，因为目前的软件选项缺乏直观的用户界面和广泛的文档。因此，我们提出了开放源代码软件包GUARDD（弛豫离散度数据的图形用户友好分析），该软件包旨在组织、自动化和增强对CPMG RD数据进行操作的分析程序（http：//code.google.com/p/guardd/）。这个基于MATLAB的程序包括一个图形用户界面，允许全局拟合多场，多温度，多相干数据，并实现χ2映射程序，通过网格搜索和蒙特卡罗方法，以提高和评估拟合精度。演示功能允许用户无缝遍历大量结果，RD模拟器功能可以帮助设计未来的实验，并作为不熟悉RD现象的教学工具。基于这些创新功能，我们预计GUARDD将填补RD NMR社区服务的明确空白。
Molecular dynamics are essential for life, and nuclear magnetic resonance (NMR) spectroscopy has been used extensively to characterize these phenomena since the 1950s. For the past 15 years, the Carr-Purcell Meiboom-Gill relaxation dispersion (CPMG RD) NMR experiment has afforded advanced NMR labs access to kinetic, thermodynamic, and structural details of protein and RNA dynamics in the crucial µs-ms time window. However, analysis of RD data is challenging because datasets are often large and require many non-linear fitting parameters, thereby confounding assessment of accuracy. Moreover, novice CPMG experimentalists face an additional barrier because current software options lack an intuitive user interface and extensive documentation. Hence, we present the open-source software package GUARDD (Graphical User-friendly Analysis of Relaxation Dispersion Data), which is designed to organize, automate, and enhance the analytical procedures which operate on CPMG RD data (http://code.google.com/p/guardd/). This MATLAB-based program includes a graphical user interface, permits global fitting to multi-field, multi-temperature, multi-coherence data, and implements χ2-mapping procedures, via grid-search and Monte Carlo methods, to enhance and assess fitting accuracy. The presentation features allow users to seamlessly traverse the large amount of results, and the RD Simulator feature can help design future experiments as well as serve as a teaching tool for those unfamiliar with RD phenomena. Based on these innovative features, we expect that GUARDD will fill a well-defined gap in service of the RD NMR community.
登录
查看更多内容
影响因子：
15
作者：
Millet, O;Loria, JP;Palmer, AG
通讯作者：
Palmer, AG
影响因子：
3.3
作者：
Hansen, D. Flemming;Vallurupalli, Pramodh;Kay, Lewis E.
通讯作者：
Kay, Lewis E.
影响因子：
14.9
作者：
Kloiber K;Spitzer R;Tollinger M;Konrat R;Kreutz C
通讯作者：
Kreutz C
影响因子：
3.3
作者：
Jee, JunGoo;Ishima, Rieko;Gronenborn, Angela M.
通讯作者：
Gronenborn, Angela M.
影响因子：
15
作者：
Korzhnev, DM;Neudecker, P;Kay, LE
通讯作者：
Kay, LE