Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Abstract

Prediction of protein stability upon amino acid substitution and discrimination of thermophilic proteins from mesophilic ones are important problems in designing stable proteins. We have developed a classification rule generator using the information about wild-type, mutant, three neighboring residues and experimentally observed stability data. Utilizing the rules, we have developed a method based on decision tree for discriminating the stabilizing and destabilizing mutants and predicting protein stability changes upon single point mutations, which showed an accuracy of 82% and a correlation of 0.70, respectively. In addition, we have systematically analyzed the characteristic features of amino acid residues in 3075 mesophilic and 1609 thermophilic proteins belonging to 9 and 15 families, respectively, and developed methods for discriminating them. The method based on neural network could discrimi-nate them at the 5-fold cross-validation accuracy of 89% in a dataset of 4684 proteins and 91% in a test set of 707 proteins.

Original languageEnglish
Title of host publication3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008
Pages1-12
Number of pages12
Volume5265 LNBI
DOIs
Publication statusPublished - 2008 Dec 5
Event3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008 - Melbourne, VIC, Australia
Duration: 2008 Oct 152008 Oct 17

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5265 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008
CountryAustralia
CityMelbourne, VIC
Period08-10-1508-10-17

Fingerprint

Mutant
Discrimination
Proteins
Protein
Prediction
Amino Acids
Amino acids
Classification Rules
Test Set
Decision trees
Cross-validation
Decision tree
Substitution
Mutation
Fold
Substitution reactions
Generator
Neural Networks
Neural networks

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Gromiha, M. M., Huang, L. T., & Lai, L-F. (2008). Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins. In 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008 (Vol. 5265 LNBI, pp. 1-12). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5265 LNBI). https://doi.org/10.1007/978-3-540-88436-1-1
Gromiha, M. Michael ; Huang, Liang Tsung ; Lai, Lien-Fu. / Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins. 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008. Vol. 5265 LNBI 2008. pp. 1-12 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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Gromiha, MM, Huang, LT & Lai, L-F 2008, Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins. in 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008. vol. 5265 LNBI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5265 LNBI, pp. 1-12, 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008, Melbourne, VIC, Australia, 08-10-15. https://doi.org/10.1007/978-3-540-88436-1-1

Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins. / Gromiha, M. Michael; Huang, Liang Tsung; Lai, Lien-Fu.

3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008. Vol. 5265 LNBI 2008. p. 1-12 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5265 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Gromiha MM, Huang LT, Lai L-F. Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins. In 3rd IAPR International Conference on Pattern Recognition in Bioinformatics, PRIB 2008. Vol. 5265 LNBI. 2008. p. 1-12. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-540-88436-1-1