Assessment of template-based modeling of protein structure in CASP11
Assessment of template-based modeling of protein structure in CASP11
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DOI：
10.1002/prot.25049
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发表时间：
2016-09-01
影响因子：
2.9
通讯作者：
Dunbrack, Roland L., Jr.
中科院分区：
文献类型：
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作者：
Modi, Vivek;Xu, Qifang;Dunbrack, Roland L., Jr.
我们提出了对CASP11基于模板的建模（TBM）类别（蛋白质结构预测的关键评估）中提交的预测的评估。模型质量是根据包括侧链在内的所有原子的全局和局部精度度量来判断的。基于模型1预测的39个人类服务器目标的顶级组是LEER、Zhang、LEE、MULTICOM和Zhang- server。基于模型1预测的服务器组在81个目标上排名靠前的组是Zhang-Server、nns、BAKER-ROSETTASERVER、QUARK和myprotein-me。在CASP11中，大多数靶标的最佳模型等于或优于蛋白质数据库中可用的最佳模板，即使对于模板较差的靶标也是如此。CASP11中的总体性能与CASP10中的预测因子的性能相似，在最难目标上的性能略好。对于大多数目标，评估指标呈现双峰概率密度分布。对每个目标的RMSD矩阵进行多维尺度变换，通常会发现与目标结构相似的模型只有一个聚类，其模态在GDT-TS密度的40 ~ 90之间；模型分布广泛，彼此之间以及与实验结构高度发散，密度模态在GDT-TS值的20附近。密度峰值处的模型要么是褶皱完全错误的紧致模型，要么是高度非紧致模型。结果表明，在未来的CASP TBM评估中，应该采用密度驱动的方法，考虑这些分布的双峰性质，而不是假设单峰高斯分布的Z分数。(C) 2016 Wiley期刊公司
We present the assessment of predictions submitted in the template-based modeling (TBM) category of CASP11 (Critical Assessment of Protein Structure Prediction). Model quality was judged on the basis of global and local measures of accuracy on all atoms including side chains. The top groups on 39 human-server targets based on model 1 predictions were LEER, Zhang, LEE, MULTICOM, and Zhang-Server. The top groups on 81 targets by server groups based on model 1 predictions were Zhang-Server, nns, BAKER-ROSETTASERVER, QUARK, and myprotein-me. In CASP11, the best models for most targets were equal to or better than the best template available in the Protein Data Bank, even for targets with poor templates. The overall performance in CASP11 is similar to the performance of predictors in CASP10 with slightly better performance on the hardest targets. For most targets, assessment measures exhibited bimodal probability density distributions. Multidimensional scaling of an RMSD matrix for each target typically revealed a single cluster with models similar to the target structure, with a mode in the GDT-TS density between 40 and 90, and a wide distribution of models highly divergent from each other and from the experimental structure, with density mode at a GDT-TS value of similar to 20. The models in this peak in the density were either compact models with entirely the wrong fold, or highly non-compact models. The results argue for a density-driven approach in future CASP TBM assessments that accounts for the bimodal nature of these distributions instead of Z scores, which assume a unimodal, Gaussian distribution. (C) 2016 Wiley Periodicals, Inc.