Predicting protein crystallization using a simple scoring card method

Watshara Shoombuatong, Hui Ling Huang, Jeerayut Chaijaruwanich, Phasit Charoenkwan, Hua Chin Lee, Shinn-Ying Ho

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

9 Scopus citations

Abstract

Many computational methods have been developed to predict protein crystallization. Most methods use amino acid and dipeptide compositions as part of the informative features. To advance the prediction accuracy, the support vector machine (SVM) based classifiers and ensemble approaches were effective and commonly-used techniques. However, these techniques suffer from the low interpretation ability of insight into crystallization. In this study, we utilize a newly-developed scoring card method (SCM) with a dipeptide composition feature to predict protein crystallization. This SCM classifier obtains prediction results 74%, 0.55 and 0.83 for accuracy, sensitivity and specificity, respectively, which is comparable to the SVM classifier using the same benchmarks. The experimental results show that the SCM classifier has advantages of simplicity, high interpretability, and high accuracy in predicting protein crystallization, compared with existing SVM-basedensemble classifiers.

Original languageEnglish
Title of host publicationProceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2013 - 2013 IEEE Symposium Series on Computational Intelligence, SSCI 2013
Pages23-30
Number of pages8
DOIs
StatePublished - 10 Oct 2013
Event10th Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2013 - 2013 IEEE Symposium Series on Computational Intelligence, SSCI 2013 - Singapore, Singapore
Duration: 16 Apr 201319 Apr 2013

Publication series

NameProceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2013 - 2013 IEEE Symposium Series on Computational Intelligence, SSCI 2013

Conference

Conference10th Annual IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, CIBCB 2013 - 2013 IEEE Symposium Series on Computational Intelligence, SSCI 2013
CountrySingapore
CitySingapore
Period16/04/1319/04/13

Keywords

  • genetic algorithm
  • protein crystallization
  • protein prediction
  • scoring card method

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