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This article is part of the supplement: The 2009 International Conference on Bioinformatics & Computational Biology (BioComp 2009)

Open Access Open Badges Research

Sequence feature-based prediction of protein stability changes upon amino acid substitutions

Shaolei Teng1, Anand K Srivastava12 and Liangjiang Wang12*

Author Affiliations

1 Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA

2 J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA

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BMC Genomics 2010, 11(Suppl 2):S5  doi:10.1186/1471-2164-11-S2-S5

Published: 2 November 2010



Protein destabilization is a common mechanism by which amino acid substitutions cause human diseases. Although several machine learning methods have been reported for predicting protein stability changes upon amino acid substitutions, the previous studies did not utilize relevant sequence features representing biological knowledge for classifier construction.


In this study, a new machine learning method has been developed for sequence feature-based prediction of protein stability changes upon amino acid substitutions. Support vector machines were trained with data from experimental studies on the free energy change of protein stability upon mutations. To construct accurate classifiers, twenty sequence features were examined for input vector encoding. It was shown that classifier performance varied significantly by using different sequence features. The most accurate classifier in this study was constructed using a combination of six sequence features. This classifier achieved an overall accuracy of 84.59% with 70.29% sensitivity and 90.98% specificity.


Relevant sequence features can be used to accurately predict protein stability changes upon amino acid substitutions. Predictive results at this level of accuracy may provide useful information to distinguish between deleterious and tolerant alterations in disease candidate genes. To make the classifier accessible to the genetics research community, we have developed a new web server, called MuStab ( webcite).