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Bioinformatics Advance Access originally published online on March 22, 2007
Bioinformatics 2007 23(10):1292-1293; doi:10.1093/bioinformatics/btm100
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations

Liang-Tsung Huang 1,2, M. Michael Gromiha 3,* and Shinn-Ying Ho 4

1Department of Computer Science and Information Engineering, Ming-Dao University, Changhua 523, 2Institute of Information Engineering and Computer Science, Feng-Chia University, Taichung 407, Taiwan, 3Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan and 4Department of Biological Science and Technology, and Institute of Bioinformatics, National Chiao-Tung University, Hsinchu 300, Taiwan

*To whom correspondence should be addressed.


  Abstract

Summary: We have developed a web server, iPTREE-STAB for discriminating the stability of proteins (stabilizing or destabilizing) and predicting their stability changes ({Delta}{Delta}G) upon single amino acid substitutions from amino acid sequence. The discrimination and prediction are mainly based on decision tree coupled with adaptive boosting algorithm, and classification and regression tree, respectively, using three neighboring residues of the mutant site along N- and C-terminals. Our method showed an accuracy of 82% for discriminating the stabilizing and destabilizing mutants, and a correlation of 0.70 for predicting protein stability changes upon mutations.

Availability: http://bioinformatics.myweb.hinet.net/iptree.htm

Contact: michael-gromiha{at}aist.go.jp

Supplementary information: Dataset and other details are given.

Associate Editor: Burkhard Rost

Received on January 9, 2007; revised on February 18, 2007; accepted on March 8, 2007

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