iHyd-PseAAC: Predicting Hydroxyproline and Hydroxylysine in Proteins by Incorporating Dipeptide Position-Specific Propensity into Pseudo Amino Acid Composition
| Autor: | Yan Xu, Xiaojian Shao, Kuo-Chen Chou, Nai-Yang Deng, Xin Wen |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Lysine
Hydroxylysine Article Catalysis lcsh:Chemistry Inorganic Chemistry Hydroxylation User-Computer Interface chemistry.chemical_compound Protein hydroxylation Protein sequencing PseAAC Amino Acids Physical and Theoretical Chemistry Databases Protein lcsh:QH301-705.5 Molecular Biology Pseudo amino acid composition Spectroscopy chemistry.chemical_classification Internet Dipeptide PTMs Organic Chemistry Proteins Dipeptides General Medicine Computer Science Applications Amino acid Hydroxyproline HyP HyL discriminant function algorithm lcsh:Biology (General) lcsh:QD1-999 chemistry Biochemistry Protein Processing Post-Translational Algorithms |
| Zdroj: | International Journal of Molecular Sciences; Volume 15; Issue 5; Pages: 7594-7610 International Journal of Molecular Sciences, Vol 15, Iss 5, Pp 7594-7610 (2014) International Journal of Molecular Sciences |
| ISSN: | 1422-0067 |
| DOI: | 10.3390/ijms15057594 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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