CASP9 target classification.
CASP9 target classification.
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DOI：
10.1002/prot.23190
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发表时间：
2011
影响因子：
2.9
通讯作者：
Grishin, Nick V.
中科院分区：
文献类型：
--
作者：
Kinch, Lisa N.;Shi, Shuoyong;Cheng, Hua;Cong, Qian;Pei, Jimin;Mariani, Valerio;Schwede, Torsten;Grishin, Nick V.
关键词：
第九轮蛋白质结构预测的关键评估(CASP9)旨在评估129个实验确定的蛋白质结构的预测。为了评估三级结构预测，将这些目标结构划分为基于领域的评估单元，然后将其分为两个评估类别：基于模板的建模(TBM)和无模板建模(FM)。CASP9靶标被分成结构紧凑的进化模块的结构域。对于具有多个已定义域的目标，是否将结构拆分为域进行评估是基于服务器性能的决定。根据目标域与现有模板的进化关联性以及由服务器性能指示的难度级别对目标域进行分类。具有序列相关模板且服务器预测性能较高的目标域被归类为TMB，而没有可识别模板且服务器性能较低的目标域被归类为FM。然而，使用这些概括进行分类导致CASP9评估类别之间的边界变得模糊。因此，FM类别包括那些没有序列可检测模板的域(25个目标域)以及一些难以检测到模板的域，它们的预测能力与没有模板的域一样差(5个目标域)。讨论了几个有趣的例子，包括具有表现出不寻常结构差异的序列相关模板的靶、具有不能被序列检测的同源或相似结构模板的靶以及具有新折叠的靶。
The Critical Assessment of Protein Structure Prediction round 9 (CASP9) aimed to evaluate predictions for 129 experimentally determined protein structures. To assess tertiary structure predictions, these target structures were divided into domain-based evaluation units that were then classified into two assessment categories: template based modeling (TBM) and template free modeling (FM). CASP9 targets were split into domains of structurally compact evolutionary modules. For the targets with more than one defined domain, the decision to split structures into domains for evaluation was based on server performance. Target domains were categorized based on their evolutionary relatedness to existing templates as well as their difficulty levels indicated by server performance. Those target domains with sequence-related templates and high server prediction performance were classified as TMB, while those targets without identifiable templates and low server performance were classified as FM. However, using these generalizations for classification resulted in a blurred boundary between CASP9 assessment categories. Thus, the FM category included those domains without sequence detectable templates (25 target domains) as well as some domains with difficult to detect templates whose predictions were as poor as those without templates (5 target domains). Several interesting examples are discussed, including targets with sequence related templates that exhibit unusual structural differences, targets with homologous or analogous structure templates that are not detectable by sequence, and targets with new folds.
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