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Protein secondary structure prediction (PSSP) using different machine algorithms

Authors
  • Afify, Heba M.1
  • Abdelhalim, Mohamed B.2
  • Mabrouk, Mai S.3
  • Sayed, Ahmed Y.4
  • 1 Higher Institute of Engineering, El-Shorouk City, Cairo, Egypt , El-Shorouk City (Egypt)
  • 2 Arab Academy for Science Technology and Maritime Transport (AASTMT), Cairo, Egypt , Cairo (Egypt)
  • 3 Misr University for Science and Technology (MUST), 6th of October City, Egypt , 6th of October City (Egypt)
  • 4 Halwan University, Cairo, Egypt , Cairo (Egypt)
Type
Published Article
Journal
Egyptian Journal of Medical Human Genetics
Publisher
Springer Berlin Heidelberg
Publication Date
Jun 07, 2021
Volume
22
Issue
1
Identifiers
DOI: 10.1186/s43042-021-00173-w
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundThe computational biology approach has advanced exponentially in protein secondary structure prediction (PSSP), which is vital for the pharmaceutical industry. Extracting protein structure from the laboratory has insufficient information for PSSP that is used in bioinformatics studies. In this paper, the support vector machine (SVM) model and decision tree are presented on the RS126 dataset to address the problem of PSSP. A decision tree is applied for the SVM outcome to obtain the relevant guidelines possible for PSSP. Furthermore, the number of produced rules was fairly small, and they show a greater degree of comprehensibility compared to other rules. Several of the proposed principles have compelling and relevant biological clarification.ResultsThe results confirmed that the existence of a particular amino acid in a protein sequence increases the stability for the forecast of protein secondary structure. The suggested algorithm achieved 85% accuracy for the E|~E classifier.ConclusionsThe proposed rules can be very important in managing wet laboratory experiments intended at determining protein secondary structure. Lastly, future work will focus mainly on large protein datasets without overfitting and expand the amount of extracted regulations for PSSP.

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