Department of Computer Science & Engineering, University of South Carolina, Columbia, SC 29208, USA.
BMC Bioinformatics. 2013 Oct 7;14:302. doi: 10.1186/1471-2105-14-302.
Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. The REDCAT software package was previously introduced for the analysis of molecular structures using RDC data. Here we report additional features that have been included in this software package in order to expand the scope of its analyses. We first discuss the features that enhance REDCATs user-friendly nature, such as the integration of a number of analyses into one single operation and enabling convenient examination of a structural ensemble in order to identify the most suitable structure. We then describe the new features which expand the scope of RDC analyses, performing exercises that utilize both synthetic and experimental data to illustrate and evaluate different features with regard to structure refinement and structure validation.
We establish the seamless interaction that takes place between REDCAT, VMD, and Xplor-NIH in demonstrations that utilize our newly developed REDCAT-VMD and XplorGUI interfaces. These modules enable visualization of RDC analysis results on the molecular structure displayed in VMD and refinement of structures with Xplor-NIH, respectively. We also highlight REDCAT's Error-Analysis feature in reporting the localized fitness of a structure to RDC data, which provides a more effective means of recognizing local structural anomalies. This allows for structurally sound regions of a molecule to be identified, and for any refinement efforts to be focused solely on locally distorted regions.
The newly engineered REDCAT software package, which is available for download via the WWW from http://ifestos.cse.sc.edu, has been developed in the Object Oriented C++ environment. Our most recent enhancements to REDCAT serve to provide a more complete RDC analysis suite, while also accommodating a more user-friendly experience, and will be of great interest to the community of researchers and developers since it hides the complications of software development.
在过去的二十年中，残剩偶极耦合（RDC）已经成为一种有价值的实验约束条件，可用于研究生物大分子和复合物的结构和动态。REDCAT 软件包以前是为了使用 RDC 数据分析分子结构而引入的。在这里，我们报告了该软件包中包含的其他功能，以扩展其分析范围。我们首先讨论了增强 REDCAT 用户友好性的功能，例如将多项分析集成到一个操作中，并能够方便地检查结构集合，以确定最合适的结构。然后，我们描述了扩展 RDC 分析范围的新功能，通过使用合成和实验数据进行练习，来演示和评估不同功能在结构精修和结构验证方面的表现。
我们通过使用我们新开发的 REDCAT-VMD 和 XplorGUI 接口进行的演示，建立了 REDCAT、VMD 和 Xplor-NIH 之间的无缝交互。这些模块分别使 RDC 分析结果能够在 VMD 中显示的分子结构上进行可视化，以及使用 Xplor-NIH 对结构进行精修。我们还强调了 REDCAT 的错误分析功能，该功能报告了结构对 RDC 数据的局部拟合程度，这提供了一种更有效的识别局部结构异常的方法。这可以识别分子中结构合理的区域，并将任何精修工作仅集中在局部变形的区域上。
可从 WWW 上的 http://ifestos.cse.sc.edu 下载的新设计的 REDCAT 软件包是在面向对象的 C++环境中开发的。我们对 REDCAT 的最新增强功能提供了更完整的 RDC 分析套件，同时也提供了更用户友好的体验，对于研究人员和开发人员来说将非常感兴趣，因为它隐藏了软件开发的复杂性。
