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iPhosY-PseAAC: identify phosphotyrosine sites by incorporating sequence statistical moments into PseAAC

  • Yaser Daanial Khan
  • Nouman Rasool
  • Waqar Hussain
  • Sher Afzal Khan
  • Kuo-Chen Chou
Original Article
  • 18 Downloads

Abstract

Protein phosphorylation is one of the most fundamental types of post-translational modifications and it plays a vital role in various cellular processes of eukaryotes. Among three types of phosphorylation i.e. serine, threonine and tyrosine phosphorylation, tyrosine phosphorylation is one of the most frequent and it is important for mediation of signal transduction in eukaryotic cells. Site-directed mutagenesis and mass spectrometry help in the experimental determination of cellular signalling networks, however, these techniques are costly, time taking and labour associated. Thus, efficient and accurate prediction of these sites through computational approaches can be beneficial to reduce cost and time. Here, we present a more accurate and efficient sequence-based computational method for prediction of phosphotyrosine (PhosY) sites by incorporation of statistical moments into PseAAC. The study is carried out based on Chou’s 5-step rule, and various position-composition relative features are used to train a neural network for the prediction purpose. Validation of results through Jackknife testing is performed to validate the results of the proposed prediction method. Overall accuracy validated through Jackknife testing was calculated 93.9%. These results suggest that the proposed prediction model can play a fundamental role in the prediction of PhosY sites in an accurate and efficient way.

Keywords

Phosphotyrosine Prediction PseAAC Statistical moments Neural network 

Notes

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11033_2018_4417_MOESM1_ESM.xlsx (203 kb)
Supplementary material 1 (XLSX 203 KB)—Supporting Information S1.xlsx: The benchmark dataset contains 1858 positive samples and 2023 negative samples

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Yaser Daanial Khan
    • 1
  • Nouman Rasool
    • 2
    • 5
  • Waqar Hussain
    • 1
  • Sher Afzal Khan
    • 3
    • 6
  • Kuo-Chen Chou
    • 4
  1. 1.Department of Computer Science, School of Systems and TechnologyUniversity of Management and Technology, C-II Johar TownLahorePakistan
  2. 2.Department of Life Sciences, School of ScienceUniversity of Management and TechnologyLahorePakistan
  3. 3.Faculty of Computing and Information Technology in RabighKing Abdul Aziz UniversityJeddahKingdom of Saudi Arabia
  4. 4.Gordon Life Science InstituteBostonUSA
  5. 5.Dr Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological SciencesUniversity of KarachiKarachiPakistan
  6. 6.Department of Computer SciencesAbdul Wali Khan UniversityMardanPakistan

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