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. 2014 May 5;15(5):7594-610.
doi: 10.3390/ijms15057594.

iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition

Yan Xu  1 , Xin Wen  2 , Xiao-Jian Shao  3 , Nai-Yang Deng  4 , Kuo-Chen Chou  5
Affiliations

iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition

Yan Xu et al. Int J Mol Sci. .

Abstract

Post-translational modifications (PTMs) play crucial roles in various cell functions and biological processes. Protein hydroxylation is one type of PTM that usually occurs at the sites of proline and lysine. Given an uncharacterized protein sequence, which site of its Pro (or Lys) can be hydroxylated and which site cannot? This is a challenging problem, not only for in-depth understanding of the hydroxylation mechanism, but also for drug development, because protein hydroxylation is closely relevant to major diseases, such as stomach and lung cancers. With the avalanche of protein sequences generated in the post-genomic age, it is highly desired to develop computational methods to address this problem. In view of this, a new predictor called "iHyd-PseAAC" (identify hydroxylation by pseudo amino acid composition) was proposed by incorporating the dipeptide position-specific propensity into the general form of pseudo amino acid composition. It was demonstrated by rigorous cross-validation tests on stringent benchmark datasets that the new predictor is quite promising and may become a useful high throughput tool in this area. A user-friendly web-server for iHyd-PseAAC is accessible at http://app.aporc.org/iHyd-PseAAC/. Furthermore, for the convenience of the majority of experimental scientists, a step-by-step guide on how to use the web-server is given. Users can easily obtain their desired results by following these steps without the need of understanding the complicated mathematical equations presented in this paper just for its integrity.

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Figures

Figure 1.
Figure 1.
Schematic drawing to show protein hydroxylation occurring at (a) proline and (b) lysine to form hydroxyproline (HyP) and hydroxylysine (HyL), respectively.
Figure 2.
Figure 2.
An illustration to show Chou’s scheme for peptides with (2ξ + 1) residues and their centers being (a) proline and (b) lysine. Adapted from Chou [27,29] with permission.
Figure 3.
Figure 3.
Flowchart to show the process of how the iHyd-PseAAC (identify hydroxylation pseudo amino acid composition) predictor works in identifying the hydroxylated sites in proteins. PSDP, position-specific dipeptide propensity.
Figure 4.
Figure 4.
The top-page of the web-server, iHud-PseAAC, at http://app.aporc.org/iHyd-PseAAC/.
See this image and copyright information in PMC

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