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,
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