Predicting changes in protein thermostability brought about by single- or multi-site mutations

BMC Bioinformatics

Software

Ningfeng Wu¹  Xiaoyu Chu¹  Yunliu Fan¹  Jian Tian¹ 

[1] Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, 100081, Beijing, China;

关键词: Support Vector Machine;    Random Forest;    Support Vector Regression;    Reliability Index;    Machine Learning Method;   

DOI  :  10.1186/1471-2105-11-370

 received in 2010-03-29, accepted in 2010-07-02,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundAn important aspect of protein design is the ability to predict changes in protein thermostability arising from single- or multi-site mutations. Protein thermostability is reflected in the change in free energy (ΔΔG) of thermal denaturation.ResultsWe have developed predictive software, Prethermut, based on machine learning methods, to predict the effect of single- or multi-site mutations on protein thermostability. The input vector of Prethermut is based on known structural changes and empirical measurements of changes in potential energy due to protein mutations. Using a 10-fold cross validation test on the M-dataset, consisting of 3366 mutants proteins from ProTherm, the classification accuracy of random forests and the regression accuracy of random forest regression were slightly better than support vector machines and support vector regression, whereas the overall accuracy of classification and the Pearson correlation coefficient of regression were 79.2% and 0.72, respectively. Prethermut performs better on proteins containing multi-site mutations than those with single mutations.ConclusionsThe performance of Prethermut indicates that it is a useful tool for predicting changes in protein thermostability brought about by single- or multi-site mutations and will be valuable in the rational design of proteins.

【 授权许可】

Unknown   
© Tian et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.