Int. J. Mol. Sci. 2014, 15(5), 7594-7610; doi:10.3390/ijms15057594
Article

iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition

1,5,* email, 1email, 2email, 3email and 4,5email
Received: 7 February 2014; in revised form: 4 April 2014 / Accepted: 17 April 2014 / Published: 5 May 2014
(This article belongs to the collection Proteins and Protein-Ligand Interactions)
View Full-Text   |   Download PDF [1218 KB, uploaded 19 June 2014]
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.
Keywords: PTMs; HyP; HyL; PseAAC; discriminant function algorithm
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Export to BibTeX |
EndNote


MDPI and ACS Style

Xu, Y.; Wen, X.; Shao, X.-J.; Deng, N.-Y.; Chou, K.-C. iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition. Int. J. Mol. Sci. 2014, 15, 7594-7610.

AMA Style

Xu Y, Wen X, Shao X-J, Deng N-Y, Chou K-C. iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition. International Journal of Molecular Sciences. 2014; 15(5):7594-7610.

Chicago/Turabian Style

Xu, Yan; Wen, Xin; Shao, Xiao-Jian; Deng, Nai-Yang; Chou, Kuo-Chen. 2014. "iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition." Int. J. Mol. Sci. 15, no. 5: 7594-7610.


Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert