Toward the estimation of the absolute quality of individual protein structure models.
Toward the estimation of the absolute quality of individual protein structure models.
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DOI：
10.1093/bioinformatics/btq662
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发表时间：
2011-02-01
期刊：
影响因子：
--
通讯作者：
Schwede T
中科院分区：
文献类型：
--
作者：
Benkert P;Biasini M;Schwede T
动机：蛋白质结构的质量评估是实验结构验证的重要部分，并且在蛋白质结构预测中起着至关重要的作用，因为预测的模型可能包含大量错误。当前大多数评分函数主要是为了对同一序列的不同模型进行排序以支持模型选择，而单个蛋白质模型的绝对质量预测在该领域很少受到关注。然而，可靠的绝对质量评估对于评估模型对特定生物医学应用的适用性至关重要。
结果：在这项工作中，我们提出了一种新的蛋白质模型质量的绝对衡量标准，它对模型中观察到的结构特征的“天然程度”进行估计，并描述了给定模型与实验结构质量相当的可能性。基于QMEAN评分函数的模型质量评估根据相互作用的数量进行了归一化。由此产生的评分函数与蛋白质的大小无关，因此可用于评估单体和整个寡聚体组装。然后，将单个模型的模型质量分数与高分辨率晶体结构获得的分数相比，表示为“Z分数”。我们证明了新引入的QMEAN Z分数能够检测包含显著错误的实验解析的蛋白质结构，以及评估理论蛋白质模型。
在对蛋白质数据库（PDB）中所有实验结构进行的全面QMEAN Z分数分析中，膜蛋白聚集在分数谱的一侧，热稳定蛋白聚集在另一侧。来自嗜热生物海栖热袍菌（Thermatoga maritima）的蛋白质在与它们的中温同源物成对比较时，获得了显著更高的QMEAN Z分数，这强调了QMEAN Z分数作为蛋白质稳定性估计的重要性。
可用性：Z分数计算已集成到QMEAN服务器中，网址为：http://swissmodel.expasy.org/qmean。
联系人：torsten.schwede@unibas.ch
补充信息：补充数据可在Bioinformatics在线获取。
Motivation: Quality assessment of protein structures is an important part of experimental structure validation and plays a crucial role in protein structure prediction, where the predicted models may contain substantial errors. Most current scoring functions are primarily designed to rank alternative models of the same sequence supporting model selection, whereas the prediction of the absolute quality of an individual protein model has received little attention in the field. However, reliable absolute quality estimates are crucial to assess the suitability of a model for specific biomedical applications. Results: In this work, we present a new absolute measure for the quality of protein models, which provides an estimate of the ‘degree of nativeness’ of the structural features observed in a model and describes the likelihood that a given model is of comparable quality to experimental structures. Model quality estimates based on the QMEAN scoring function were normalized with respect to the number of interactions. The resulting scoring function is independent of the size of the protein and may therefore be used to assess both monomers and entire oligomeric assemblies. Model quality scores for individual models are then expressed as ‘Z-scores’ in comparison to scores obtained for high-resolution crystal structures. We demonstrate the ability of the newly introduced QMEAN Z-score to detect experimentally solved protein structures containing significant errors, as well as to evaluate theoretical protein models. In a comprehensive QMEAN Z-score analysis of all experimental structures in the PDB, membrane proteins accumulate on one side of the score spectrum and thermostable proteins on the other. Proteins from the thermophilic organism Thermatoga maritima received significantly higher QMEAN Z-scores in a pairwise comparison with their homologous mesophilic counterparts, underlining the significance of the QMEAN Z-score as an estimate of protein stability. Availability: The Z-score calculation has been integrated in the QMEAN server available at: http://swissmodel.expasy.org/qmean. Contact: torsten.schwede@unibas.ch Supplementary information: Supplementary data are available at Bioinformatics online.
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