iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC

Title:iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC

Volume: 13 Issue: 6

Author(s): Yan Xu, Zu Wang, Chunhui Li*Kuo-Chen Chou

Affiliation:

• School of Mathematics and Statistics, Beijing Institute of Technology, Beijing 100081,China

Keywords: Autoimmune disease, cysteine prenylation, protein C-terminal, PseAAC, SVM, web-server.

Abstract: Background: Occurring at the cysteine residue in the C-terminal of a protein, prenylation is a special kind of post-translational modification (PTM), which may play a key role for statin in altering immune function. Therefore, knowledge of the prenylation sites in proteins is important for drug development as well as for in-depth understanding the biological process concerned.

Objective: Given a query protein whose C-terminal contains some cysteine residues, which one can be of prenylation or none of them can be prenylated?

Methods: To address this problem, we have developed a new predictor, called “iPreny-PseAAC”, by incorporating two tiers of sequence pair coupling effects into the general form of PseAAC (pseudo amino acid composition).

Results: It has been observed by four different cross-validation approaches that all the important indexes in reflecting its prediction quality are quite high and fully consistent to each other.

Conclusion: It is anticipated that the iPreny-PseAAC predictor holds very high potential to become a useful high throughput tool in identifying protein C-terminal cysteine prenylation sites and the other relevant areas. To maximize the convenience for most experimental biologists, the webserver for the new predictor has been established at http://app.aporc.org/iPreny-PseAAC/, by which users can easily get their desired results without needing to go through the mathematical details involved in this paper.

Cite this article as:

Xu Yan, Wang Zu , Li Chunhui*, Chou Kuo-Chen , iPreny-PseAAC: Identify C-terminal Cysteine Prenylation Sites in Proteins by Incorporating Two Tiers of Sequence Couplings into PseAAC, Medicinal Chemistry 2017; 13 (6) . https://dx.doi.org/10.2174/1573406413666170419150052

DOI https://dx.doi.org/10.2174/1573406413666170419150052	Print ISSN 1573-4064
Publisher Name Bentham Science Publisher	Online ISSN 1875-6638