CAMRA:: Chemical shift based computer aided protein NMR assignments
CAMRA:: Chemical shift based computer aided protein NMR assignments
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DOI：
10.1023/a:1008321629308
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发表时间：
1998-10-01
影响因子：
2.7
通讯作者：
Sykes, BD
中科院分区：
文献类型：
--
作者：
Gronwald, W;Willard, L;Sykes, BD
一套名为CAMRA（计算机辅助磁共振分配）的程序已经开发出来，用于计算机辅助残基特异性蛋白质分配。CAMRA由三个单元组成：ORE、CAPTURE和PROCESS。ORE预测未分配蛋白质的NMR化学位移，使用先前分配的同源蛋白质的化学位移数据库，辅以统计衍生的化学位移数据库，其中根据其残基，原子和二级结构类型对位移进行分类。CAPTURE通过过滤掉噪声峰和其他伪影，然后将衍生的峰列表分离到不同的自旋系统，从而从核磁共振光谱中生成有效峰列表。PROCESS将ORE的化学位移预测与CAPTURE识别的自旋系统相结合，以获得残留物的特定分配。PROCESS将作业的最佳选择与分数和置信度值一起排序。与其他自动分配程序相比，CAMRA不使用任何连接信息，而是完全基于将预测位移与观察到的自旋系统相匹配。因此，CAMRA代表了一种新的和独特的方法来分配蛋白质核磁共振光谱。CAMRA在与其他分配方法结合使用以及在特殊情况下特别有用，例如在通常无法获得足够NOE信息的蛋白质中柔性区域的分配。CAMRA在属于趋化因子家族的两种中等大小的蛋白质上进行了测试。研究发现，它可以有效地预测分配，提供至少具有30%序列一致性的先前分配蛋白质的数据库。CAMRA是多功能的，可用于包括和评估异核和三维实验。
A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORE, CAPTURE and PROCESS. ORE predicts NMR chemical shifts for unassigned proteins using a chemical shift database of previously assigned homologous proteins supplemented by a statistically derived chemical shift database in which the shifts are categorized according to their residue, atom and secondary structure type. CAPTURE generates a List of valid peaks from NMR spectra by filtering out noise peaks and other artifacts and then separating the derived peak list into distinct spin systems. PROCESS combines the chemical shift predictions from ORE with the spin systems identified by CAPTURE to obtain residue specific assignments. PROCESS ranks the top choices for an assignment along with scores and confidence values. In contrast to other auto-assignment programs, CAMRA does not use any connectivity information but instead is based solely on matching predicted shifts with observed spin systems. As such, CAMRA represents a new and unique approach for the assignment of protein NMR spectra. CAMRA will be particularly useful in conjunction with other assignment methods and under special circumstances, such as the assignment of flexible regions in proteins where sufficient NOE information is generally not available. CAMRA was tested on two medium-sized proteins belonging to the chemokine family. It was found to be effective in predicting the assignment providing a database of previously assigned proteins with at least 30% sequence identity is available. CAMRA is versatile and can be used to include and evaluate heteronuclear and three-dimensional experiments.