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评估预测突变后蛋白质稳定性的计算方法:总体良好但细节欠佳。

Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details.

作者信息

Potapov Vladimir, Cohen Mati, Schreiber Gideon

机构信息

Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.

出版信息

Protein Eng Des Sel. 2009 Sep;22(9):553-60. doi: 10.1093/protein/gzp030. Epub 2009 Jun 26.

Abstract

Methods for protein modeling and design advanced rapidly in recent years. At the heart of these computational methods is an energy function that calculates the free energy of the system. Many of these functions were also developed to estimate the consequence of mutation on protein stability or binding affinity. In the current study, we chose six different methods that were previously reported as being able to predict the change in protein stability (DeltaDeltaG) upon mutation: CC/PBSA, EGAD, FoldX, I-Mutant2.0, Rosetta and Hunter. We evaluated their performance on a large set of 2156 single mutations, avoiding for each program the mutations used for training. The correlation coefficients between experimental and predicted DeltaDeltaG values were in the range of 0.59 for the best and 0.26 for the worst performing method. All the tested computational methods showed a correct trend in their predictions, but failed in providing the precise values. This is not due to lack in precision of the experimental data, which showed a correlation coefficient of 0.86 between different measurements. Combining the methods did not significantly improve prediction accuracy compared to a single method. These results suggest that there is still room for improvement, which is crucial if we want forcefields to perform better in their various tasks.

摘要

近年来,蛋白质建模与设计方法发展迅速。这些计算方法的核心是一个能计算系统自由能的能量函数。其中许多函数也是为了估计突变对蛋白质稳定性或结合亲和力的影响而开发的。在当前研究中,我们选择了六种先前报道能够预测突变后蛋白质稳定性变化(ΔΔG)的不同方法:CC/PBSA、EGAD、FoldX、I-Mutant2.0、Rosetta和Hunter。我们在一组包含2156个单突变的数据集上评估了它们的性能,每个程序都避开了用于训练的突变。实验值与预测的ΔΔG值之间的相关系数,最佳方法为0.59,最差方法为0.26。所有测试的计算方法在预测中都显示出正确的趋势,但未能提供精确的值。这并非由于实验数据缺乏精度,不同测量之间的相关系数为0.86。与单一方法相比,组合这些方法并没有显著提高预测准确性。这些结果表明仍有改进空间,如果我们希望力场在其各种任务中表现得更好,这一点至关重要。

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