SVMCRYS: An SVM approach for the prediction of protein crystallization propensity from protein sequence

Krishna Kumar Kandaswamy, Ganesan Pugalenthi, P. N. Suganthan, Rajeev Gangal

Research output: Contribution to journalArticlepeer-review

32 Scopus citations

Abstract

X-ray crystallography is the most widely used method for protein 3-dimensional structure determination. Selection of target protein that can yield high quality crystal for X-ray crystallography is a challenging task. Prediction of protein crystallization propensity from sequence information is useful for the selection of target protein for crystallization. Recently, support vector machines have been widely used to solve various biological problems. In this work, we present a SVMCRYS method which use support vector machine to classify protein sequence into 'amenable to crystallization' and 'resistant to crystallization'. SVMCRYS was trained on a dataset containing 728 sequences that gave diffraction quality crystal and 728 sequences where work had been stopped before obtaining crystal. The performance of SVMCRYS method was compared with other sequence-based crystallization prediction methods such as SECRET, CRYSTALP, OB-Score, ParCrys and XtalPred using three different datasets. SVMCRYS achieved better prediction rate with higher sensitivity and specificity. Our analysis suggests that SVMCRYS can be used to predict proteins which are amenable to crystallization and proteins which are difficult for crystallization. The SVMCRYS software, dataset and feature set can be obtained from http://www3.ntu.edu.sg/home/EPNSugan/index_files/svmcrys.htm.

Original languageEnglish (US)
Pages (from-to)423-430
Number of pages8
JournalProtein and Peptide Letters
Volume17
Issue number4
DOIs
StatePublished - 2010
Externally publishedYes

Keywords

  • Crystallization targets
  • Feature selection
  • Nuclear magnetic resonance (NMR)
  • Protein crystallization propensity
  • Recalcitrant
  • Support vector machine (SVM)
  • X-ray crystallography

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry

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