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

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

Journal Name: Medicinal Chemistry

Volume 13 , Issue 6 , 2017

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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.

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

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Article Details

VOLUME: 13
ISSUE: 6
Year: 2017
Page: [544 - 551]
Pages: 8
DOI: 10.2174/1573406413666170419150052
Price: $58

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