Sequence-based prediction of protein-protein interactions using ensemble based classifier combined with global encoding in HIV (human immunodeficiency virus)

Dian Lestari, M. I.S. Musti, Alhadi B.

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

3 Citations (Scopus)

Abstract

Human Immunodeficiency Virus is a type of intracellular obligate retrovirus that attacks the human body's immune system. This virus attacks by doing interaction between the virus and human proteins. This research uses data of amino acids sequence from protein that the feature will be modified using Global Encoding as feature extraction method and then combined with the Rotation Forest in predicting the interaction between HIV and human proteins. The Global Encoding method will first group 20 types of amino acids into 6 classes and then get 10 combinations each containing three different classes. Based on these 10 combinations, a protein sequence will be transformed into 10 characteristic sequence binaries. Each sequence characteristic is further divided into several subsets based on a partition method. Then, two types of protein descriptor, composition and transition, were extracted to represent each protein sequence and used as final input vectors for the classification method. Finally, Rotation Forest is used to predicting the class of protein interactions between humans and HIV proteins. The best model obtained in this research has an accuracy of 79.50 %, sensitivity of 79.91 %, specificity of 79.07 %, and precision of 79.77 % in predicting protein interactions between HIV and Human.

Original languageEnglish
Title of host publicationProceedings of the 3rd International Symposium on Current Progress in Mathematics and Sciences 2017, ISCPMS 2017
EditorsRatna Yuniati, Terry Mart, Ivandini T. Anggraningrum, Djoko Triyono, Kiki A. Sugeng
PublisherAmerican Institute of Physics Inc.
ISBN (Electronic)9780735417410
DOIs
Publication statusPublished - 22 Oct 2018
Event3rd International Symposium on Current Progress in Mathematics and Sciences 2017, ISCPMS 2017 - Bali, Indonesia
Duration: 26 Jul 201727 Jul 2017

Publication series

NameAIP Conference Proceedings
Volume2023
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Conference

Conference3rd International Symposium on Current Progress in Mathematics and Sciences 2017, ISCPMS 2017
CountryIndonesia
CityBali
Period26/07/1727/07/17

Keywords

  • Protein Sequence
  • Protein-Protein Interaction
  • Rotation Forest
  • Substitution Matrix Representation

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