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Bioinformatics. 2016 Oct 15;32(20):3133-3141. Epub 2016 Jun 26.

pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC.

Author information

1
Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403, China Gordon Life Science Institute, Boston, MA 02478, USA.
2
Computer Department, Jing-De-Zhen Ceramic Institute, Jing-De-Zhen 333403, China.
3
School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
4
Gordon Life Science Institute, Boston, MA 02478, USA Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.

Abstract

MOTIVATION:

Sumoylation is a post-translational modification (PTM) process, in which small ubiquitin-related modifier (SUMO) is attaching by covalent bonds to substrate protein. It is critical to many different biological processes such as replicating genome, expressing gene, localizing and stabilizing proteins; unfortunately, it is also involved with many major disorders including Alzheimer's and Parkinson's diseases. Therefore, for both basic research and drug development, it is important to identify the sumoylation sites in proteins.

RESULTS:

To address such a problem, we developed a predictor called pSumo-CD by incorporating the sequence-coupled information into the general pseudo-amino acid composition (PseAAC) and introducing the covariance discriminant (CD) algorithm, in which a bias-adjustment term, which has the function to automatically adjust the errors caused by the bias due to the imbalance of training data, had been incorporated. Rigorous cross-validations indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose.

AVAILABILITY AND IMPLEMENTATION:

For the convenience of most experimental scientists, a user-friendly web-server for pSumo-CD has been established at http://www.jci-bioinfo.cn/pSumo-CD, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.

CONTACT:

jjia@gordonlifescience.org, xxiao@gordonlifescience.org or kcchou@gordonlifescience.orgSupplementary information: Supplementary data are available at Bioinformatics online.

PMID:
27354696
DOI:
10.1093/bioinformatics/btw387
[Indexed for MEDLINE]

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