Assessment of the protein-structure refinement category in CASP8
Assessment of the protein-structure refinement category in CASP8
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DOI：
10.1002/prot.22538
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发表时间：
2009-01-01
影响因子：
2.9
通讯作者：
Dill, Ken A.
中科院分区：
文献类型：
--
作者：
MacCallum, Justin L.;Hua, Lan;Dill, Ken A.
在这里，我们总结了CASP 8中蛋白质结构精修的评估。24个小组共提炼了12种靶蛋白。对所有组和所有蛋白质进行平均，与最初的起始模型相比没有净改善。然而，现在有一些个别的研究小组，他们相对于一个开始的模型，一直在改进蛋白质结构。我们比较了各种质量评估措施，包括（i）基于标准骨架的方法，（ii）Richardson组的新方法，以及（iii）用于比较实验结构的基于集合的方法，例如NMR NOE违规和预测模型作为分子置换模板的适用性。总的来说，各种措施之间存在着普遍的相互关系。然而，存在有趣的差异。有时，与实验数据更一致的结构被GDT-TS判断为稍差。这表明，为了比较已经非常接近天然的蛋白质结构，除了基于单一结构的方法（如GDT-TS）之外，最好使用基于整体的实验衍生质量测量。
Here, we summarize the assessment of protein structure refinement in CASP8. Twenty-four groups refined a total of 12 target proteins. Averaging over all groups and all proteins, there was no net improvement over the original starting models. However, there are now some individual research groups who consistently do improve protein structures relative to a starting starting model. We compare various measures of quality assessment, including (i) standard backbone-based methods, (ii) new methods from the Richardson group, and (iii) ensemble-based methods for comparing experimental structures, such as NMR NOE violations and the suitability of the predicted models to serve as templates for molecular replacement. On the whole, there is a general correlation among various measures. However, there are interesting differences. Sometimes a structure that is in better agreement with the experimental data is judged to be slightly worse by GDT-TS. This suggests that for comparing protein structures that are already quite close to the native, it may be preferable to use ensemble-based experimentally derived measures of quality, in addition to single-structure-based methods such as GDT-TS.