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iPGK-PseAAC: Identify Lysine Phosphoglycerylation Sites in Proteins by Incorporating Four Different Tiers of Amino Acid Pairwise Coupling Information into the General PseAAC

[ Vol. 13 , Issue. 6 ]

Author(s):

Li-Ming Liu, Yan Xu and Kuo-Chen Chou   Pages 552 - 559 ( 8 )

Abstract:


Background: Occurring at Lys residues, the PGK (lysine phosphoglycerylation) is a special kind of post-translational modification (PTM). It may invert the charge potential of the modified residue and change the protein structures and functions, causing various diseases in liver, brain, and kidney.

Objective: From the angles of both basic research and drug development, we are facing a critical challenging problem: for an uncharacterized protein sequence containing many Lys residues, which ones can be of phosphoglycerylation, and which ones cannot?

Method: To address this problem, we have developed a predictor called iPGK-PseAAC by incorporating into the general PseAAC (pseudo amino acid composition) with four different tiers of amino acid pairwise coupling information, where tiers 1, 2, 3, and 4 refer to the amino acid pairwise couplings between all the 1st, 2nd, 3rd, and 4th most contiguous residues along a protein segment, respectively.

Results: Rigorous cross-validations indicated that the proposed predictor remarkably outperformed its existing counterparts.

Conclusion: The proposed predictor iPGK-PseAAC will become a very useful bioinformatics tool for medicinal chemistry. For the convenience of most experimental scientists, a user-friendly webserver for iGPK-PseAAC has been established at http://app.aporc.org/iPGK-PseAAC/, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

Keywords:

Amino acid pairwise coupling, phosphoglycerylation, PseAAC, SVM, post-translational modification (PTM), lys residues.

Affiliation:

School of Statistics, Capital University of Economics and Business, Beijing 100070, Department of Information and Computer Science, University of Science and Technology Beijing, Gordon Life Science Institute, Boston, MA 02478

Graphical Abstract:



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