Scoring function for automated assessment of protein structure template quality
Scoring function for automated assessment of protein structure template quality
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DOI：
10.1002/prot.20264
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发表时间：
2004-12-01
影响因子：
2.9
通讯作者：
Skolnick, J
中科院分区：
文献类型：
--
作者：
Zhang, Y;Skolnick, J
我们开发了一种新的评分函数，即模板建模评分（TM-score），通过扩展全局距离测试（GDT）（1）和MaxSub中使用的方法来评估蛋白质结构模板的质量和预测全长模型。（2）首先，利用蛋白质大小依赖的尺度来消除先前分数的固有蛋白质大小依赖性，并适当考虑随机蛋白质结构对。其次，不是设置特定的距离截止值并仅计算误差低于截止值的分数，而是在建议的分数中评估比对/建模中的所有残基对。为了比较各种评分函数，我们使用线程程序 PROSPECTOR_3 构建了 1489 个中小型蛋白质的大规模基准结构模板集，并使用 MODELLER 和 TASSER 构建了全长模型。与 GDT 和 MaxSub 评分函数相比，初始线程比对的 TM 分数显示出与最终全长模型质量更强的相关性。 TM 分数在最近的 CASP5 实验中被进一步用作对所有“新折叠”目标的评估，并显示与人类专家视觉评估的结果非常吻合。这些数据表明 TM 评分是对蛋白质结构预测的全自动评估的有用补充。 TM-score的可执行程序可以在http://bioinformatics.buffalo.edu/TM-score免费下载。 (C) 2004 Wiley-Liss, Inc.
We have developed a new scoring function, the template modeling score (TM-score), to assess the quality of protein structure templates and predicted full-length models by extending the approaches used in Global Distance Test (GDT)(1) and MaxSub.(2) First, a protein size-dependent scale is exploited to eliminate the inherent protein size dependence of the previous scores and appropriately account for random protein structure pairs. Second, rather than setting specific distance cutoffs and calculating only the fractions with errors below the cutoff, all residue pairs in alignment/modeling are evaluated in the proposed score. For comparison of various scoring functions, we have constructed a large-scale benchmark set of structure templates for 1489 small to medium size proteins using the threading program PROSPECTOR_3 and built the full-length models using MODELLER and TASSER. The TM-score of the initial threading alignments, compared to the GDT and MaxSub scoring functions, shows a much stronger correlation to the quality of the final full-length models. The TM-score is further exploited as an assessment of all 'new fold' targets in the recent CASP5 experiment and shows a close coincidence with the results of human-expert visual assessment. These data suggest that the TM-score is a useful complement to the fully automated assessment of protein structure predictions. The executable program of TM-score is freely downloadable at http://bioinformatics.buffalo.edu/TM-score. (C) 2004 Wiley-Liss, Inc.