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Bioinformatics Advance Access originally published online on June 17, 2009
Bioinformatics 2009 25(17):2181-2187; doi:10.1093/bioinformatics/btp370
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Reliable prediction of protein thermostability change upon double mutation from amino acid sequence

Liang-Tsung Huang 1 and M. Michael Gromiha 2,*

1 Department of Computer Science and Information Engineering, Mingdao University, Changhua 523, Taiwan and 2 Computational 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

* To whom correspondence should be addressed.


  Abstract

Summary: The accurate prediction of protein stability change upon mutation is one of the important issues for protein design. In this work, we have focused on the stability change of double mutations and systematically analyzed the wild-type and mutant residues, patterns in amino acid sequence and locations of mutants. Based on the sequence information of wild-type, mutant and three neighboring residues, we have presented a weighted decision table method (WET) for predicting the stability changes of 180 double mutants obtained from thermal ({Delta}{Delta}G) denaturation. Using 10-fold cross-validation test, our method showed a correlation of 0.75 between experimental and predicted values of stability changes, and an accuracy of 82.2% for discriminating the stabilizing and destabilizing mutants.

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

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

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on March 13, 2009; revised on June 10, 2009; accepted on June 11, 2009

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