title: Disulfide connectivity prediction based on structural information without a prior knowledge of the bonding state of cysteines.
abstract: Previous studies predicted the disulfide bonding patterns of cysteines using a prior knowledge of their bonding states. In this study, we propose a method that is based on the ensemble support vector machine (SVM), with the structural features of cysteines extracted without any prior knowledge of their bonding states. This method is useful for improving the predictive performance of disulfide bonding patterns. For comparison, the proposed method was tested with the same dataset SPX that was adopted in previous studies. The experimental results demonstrate that bridge classification and disulfide connectivity predictions achieve 96.5% and 89.2% accuracy, respectively, using the ensemble SVM model, which outperforms the traditional method (51.5% and 51.0%, respectively) and the model that is based on a single-kernel SVM classifier (94.6% and 84.4%, respectively). For protein chain and residue classifications, the sensitivity, specificity, and accuracy of ensemble and single-kernel SVM approaches are better than those of the traditional methods. The predictive performances of the ensemble SVM and single-kernel models are identical, indicating that the ensemble model can converge to the single-kernel model for some applications.
authors.affiliation: Department of Management Information System, Central Taiwan University of Science and Technology, Taichung 40601, Taiwan. Electronic address: shlin@ctust.edu.tw.
authors.forename: Hsuan-Hung
authors.initials: HH
authors.lastname: Lin
authors.forename: Jiin-Chyr
authors.initials: JC
authors.lastname: Hsu
authors.forename: Yuan-Nian
authors.initials: YN
authors.lastname: Hsu
authors.forename: Ren-Hao
authors.initials: RH
authors.lastname: Pan
authors.forename: Yung-Fu
authors.initials: YF
authors.lastname: Chen
authors.forename: Lin-Yu
authors.initials: LY
authors.lastname: Tseng
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003545:Cysteine / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D004220:Disulfides / Q000737:chemistry* / Q000378:metabolism; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D060388:Support Vector Machine
chemical_list: D004220:Disulfides; D011506:Proteins; D003545:Cysteine
keywords: Disulfide bonding pattern; Ensemble classifier; Multiple trajectory search; Support vector machine