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

Author(s): Li-Ming Liu, Yan Xu*, Kuo-Chen Chou.

Journal Name: Medicinal Chemistry

Volume 13 , Issue 6 , 2017

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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.

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Article Details

VOLUME: 13
ISSUE: 6
Year: 2017
Page: [552 - 559]
Pages: 8
DOI: 10.2174/1573406413666170515120507
Price: $58

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