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iHyd-LysSite (EPSV): Identifying Hydroxylysine Sites in Protein Using Statistical Formulation by Extracting Enhanced Position and Sequence Variant Feature Technique

Author(s):

Muhammad Khalid Mahmood, Asma Ehsan*, Yaser Daanial Khan and Kuo-Chen Chou   Pages 1 - 10 ( 10 )

Abstract:


Introduction: Hydroxylation is one of the most important post-translational modification (PTM) in cellular functions and is linked to various diseases. The addition of one of a hydroxyl group (OH) to the lysine sites produce hydroxylysine when undergoes chemical modification.

Methods: The method which is used in this study for identifying hydroxylysine sites based on powerful mathematical and statistical methodology incorporating sequence-order effect and composition of each object within protein sequences. This predictor is called "iHyd-LysSite (EPSV)" (identifying hydroxylysine sites by extracting enhanced position and sequence variant technique). The prediction of hydroxylysine sites by experimental methods are difficult, laborious and highly expensive. In silico technique is an alternative approach to identify hydroxylysine sites in proteins.

Results: The experimental results require that the predictive model should have high sensitivity and specificity values and must be more accurate. The self-consistency, independent, 10-fold cross-validation and jackknife tests are performed for validation purpose. These tests are resulted by using three renowned classifiers, neural networks (NN), random forest (RF) and support vector machine (SVM) with the demanding prediction rate. The overall predictive outcomes are extraordinarily superior than the results obtained by previous predictors. The proposed model contributed excellent prediction rate in the system for NN, RF, and SVM classifiers. The sensitivity and specificity results using all these classifiers for jackknife test are 96.08% , 94.99%, 98.16% and 97.52 %, 98.52%, 80.95%.

Conclusion: The results obtained by the proposed tool show that this method may meet the future demand of hydroxylysine sites with a better prediction rate over the existing methods.

Keywords:

Hydroxylysine, PTMs, ANN, Cross-validation.

Affiliation:

Department of Mathematics, University of the Punjab, Lahore, Department of Mathematics, University of the Punjab, Lahore, Faculty of Information Technology, University of Management and Tecnology, Lahore, Faculty of Information Technology, University of Management and Tecnology, Lahore



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