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

• DOI: 10.1007/s11033-018-4417-z
• Publication Date: 2018-10-11T12:24:12Z
• Authors: Yaser Daanial Khan; Nouman Rasool; Waqar Hussain; Sher Afzal Khan; Kuo-Chen Chou
• Keywords: 0301 basic medicine; 0303 health sciences; Biometry; Computational Biology; Sequence Analysis, DNA; Phosphoproteins; 03 medical and health sciences; Phosphothreonine; Sequence Analysis, Protein; Amino Acids; Phosphorylation; Databases, Protein; Phosphotyrosine; Protein Processing, Post-Translational; Software; Algorithms; Forecasting

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.