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蛋白质稳定性预测器的性能。

Performance of protein stability predictors.

机构信息

Institute of Medical Technology, FI-33014 University of Tampere, Finland.

出版信息

Hum Mutat. 2010 Jun;31(6):675-84. doi: 10.1002/humu.21242.

Abstract

Stability is a fundamental property affecting function, activity, and regulation of biomolecules. Stability changes are often found for mutated proteins involved in diseases. Stability predictors computationally predict protein-stability changes caused by mutations. We performed a systematic analysis of 11 online stability predictors' performances. These predictors are CUPSAT, Dmutant, FoldX, I-Mutant2.0, two versions of I-Mutant3.0 (sequence and structure versions), MultiMutate, MUpro, SCide, Scpred, and SRide. As input, 1,784 single mutations found in 80 proteins were used, and these mutations did not include those used for training. The programs' performances were also assessed according to where the mutations were found in the proteins, that is, in secondary structures and on the surface or in the core of a protein, and according to protein structure type. The extents to which the mutations altered the occupied volumes at the residue sites and the charge interactions were also characterized. The predictions of all programs were in line with the experimental data. I-Mutant3.0 (utilizing structural information), Dmutant, and FoldX were the most reliable predictors. The stability-center predictors performed with similar accuracy. However, at best, the predictions were only moderately accurate ( approximately 60%) and significantly better tools would be needed for routine analysis of mutation effects.

摘要

稳定性是影响生物分子功能、活性和调节的基本性质。在与疾病相关的突变蛋白中,通常会发现稳定性变化。稳定性预测器通过计算预测突变引起的蛋白质稳定性变化。我们对 11 种在线稳定性预测器的性能进行了系统分析。这些预测器是 CUPSAT、Dmutant、FoldX、I-Mutant2.0、I-Mutant3.0 的两个版本(序列和结构版本)、MultiMutate、MUpro、SCide、Scpred 和 SRide。作为输入,使用了在 80 种蛋白质中发现的 1784 种单突变,这些突变不包括用于训练的突变。还根据突变在蛋白质中的位置(即二级结构、蛋白质表面或核心)以及蛋白质结构类型评估了程序的性能。突变改变残基位点占据体积和电荷相互作用的程度也得到了表征。所有程序的预测都与实验数据一致。I-Mutant3.0(利用结构信息)、Dmutant 和 FoldX 是最可靠的预测器。稳定性中心预测器的准确性相似。然而,预测的准确性最高也只有中等水平(约 60%),因此需要更好的工具来常规分析突变的影响。

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