An overview of tools for the validation of protein NMR structures.
An overview of tools for the validation of protein NMR structures.
复制标题
蛋白质 NMR 结构验证工具概述。
DOI：
10.1007/s10858-013-9750-x
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发表时间：
2014
影响因子：
2.7
通讯作者：
Vuister GW
中科院分区：
文献类型：
--
作者：
Vuister GW
原子分辨率的生物分子结构为理解生物学提供了宝贵的资源。NMR光谱占PDB存储库中所有结构的11%。为了解决某些NMR衍生结构的准确性存在的严重问题，以及为了便于对实验模型进行适当的分析，提供了许多程序套件。我们讨论了这些工具中的九个：PROPERIK-NMR，PSVS，GLM-RMSD，CING，Molprobity，Vivaldi，ResProx，NMR约束分析器和QMEAN。我们评估这些程序的能力，以评估结构质量，限制和他们的违规行为，化学位移，峰值和多模型NMR合奏的处理。我们记录程序所需的输入和它们生成的输出。为了讨论它们的相对优点，我们将这些工具应用于PDB中的两个代表性例子：一个小的球形单体蛋白（来自S.金黄色葡萄球菌，PDB条目2kq 3）和小的对称同源二聚体蛋白（人肌球蛋白-X的区域，PDB条目2lw 9）。
Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11 % of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease fromS. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).