Human-readable rule generator for integrating amino acid sequence information and stability of mutant proteins

Liang Tsung Huang, Lien-Fu Lai, M. Michael Gromiha

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Most of the bioinformatics tools developed for predicting mutant protein stability appear as a black box and the relationship between amino acid sequence/structure and stability is hidden to the users. We have addressed this problem and developed a human-readable rule generator for integrating the knowledge of amino acid sequence and experimental stability change upon single mutation. Using information about the original residue, substituted residue, and three neighboring residues, classification rules have been generated to discriminate the stabilizing and destabilizing mutants and explore the basis for experimental data. These rules are human readable, and hence, the method enhances the synergy between expert knowledge and computational system. Furthermore, the performance of the rules has been assessed on a nonredundant data set of 1,859 mutants and we obtained an accuracy of 80 percent using cross validation. The results showed that the method could be effectively used as a tool for both knowledge discovery and predicting mutant protein stability. We have developed a Web for classification rule generator and it is freely available at http://bioinformatics.myweb.hinet.net/irobot.htm.

Original languageEnglish
Article number4693706
Pages (from-to)681-687
Number of pages7
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume7
Issue number4
DOIs
Publication statusPublished - 2010 Jul 2

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Protein Stability
Mutant Proteins
Amino Acid Sequence
Computational Biology
Mutant
Amino acids
Generator
Proteins
Protein
Classification Rules
Bioinformatics
Mutation
Synergy
Knowledge Discovery
Black Box
Cross-validation
Percent
Data mining
Experimental Data
Human

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics
  • Applied Mathematics

Cite this

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Human-readable rule generator for integrating amino acid sequence information and stability of mutant proteins. / Huang, Liang Tsung; Lai, Lien-Fu; Gromiha, M. Michael.

In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 7, No. 4, 4693706, 02.07.2010, p. 681-687.

Research output: Contribution to journalArticle

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