KinFold

Local probes of macromolecular structure are measurements that are sensitive to the environment of a relatively small region within a macromolecule. These include, but are not limited to, NMR deuterium exchange and shift perturbation analysis, Fluorescence Resonance Energy Transfer (FRET), and RNA/DNA protein footprinting. The separate transitions reported by individual probes yield unique insight into folding intermediates. While simultaneous acquisition of many unique local transitions provides a cornucopia of information, creating an accurate global description of folding that remains faithful to local details is very challenging. This software package can be used to analyze such data. Initially, the data is clustered to identify major common transitions. Then, all possible kinetic model topologies are generated and tested to identify the best fitting kinetic model. The software creates a number of graphs and figures to explain the data. <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=81#pack_84">kinfold </a> </li> <li> <a href="https://simtk.org/frs?group_id=81#pack_596">Kinfold2.2 </a> : An optimized programing of Kinfold1.0 that is capable of processing up to 5 intermediates. one to three intermediates have the possibility to be processed on a desktop computer instead of on a multiple node cluster. This portion also uses an analytical solution to the folding equations. </li> <li> <a href="https://simtk.org/frs?group_id=81#pack_1034">Standalone Kinfold </a> : This is a stand alone package for OSX for Kinfold that can be run without matlab installed. MCR should be installed first which is included in the package </li> </ul>

对大分子结构进行局部探针测量，这些测量对大分子内部相对较小区域的微环境敏感。此类测量包括但不限于核磁共振氘交换和位移扰动分析、荧光共振能量转移（FRET）以及RNA/DNA蛋白足迹分析。单个探针报告的独立转换提供了对折叠中间体的独特见解。虽然同时获取众多独特的局部转换可以提供丰富的信息，但创建一个既忠实于局部细节又准确描述折叠全局过程的描述极具挑战性。本软件包可用于分析此类数据。最初，数据被聚类以识别主要共有转换。然后，生成并测试所有可能的动力模型拓扑结构，以确定最佳拟合动力模型。软件创建了一系列图表和图形来解释数据。该项目包含以下软件/数据包：
<ul>
<li><a href="https://simtk.org/frs?group_id=81#pack_84">kinfold</a></li>
<li><a href="https://simtk.org/frs?group_id=81#pack_596">Kinfold2.2</a>：对Kinfold1.0进行优化的程序，能够处理多达5个中间体。其中一到三个中间体有可能在桌面计算机上而非在多节点集群上处理。本部分还使用了折叠方程的分析解。</li>
<li><a href="https://simtk.org/frs?group_id=81#pack_1034">Standalone Kinfold</a>：这是一个独立的OSX包，用于Kinfold，可以在不安装Matlab的情况下运行。首先应安装MCR，它包含在包内。</li>
</ul>