iUbiq-Lys: prediction of lysine ubiquitination sites in proteins by extracting sequence evolution information via a gray system model

Abstract

As one of the most important posttranslational modifications (PTMs), ubiquitination plays an important role in regulating varieties of biological processes, such as signal transduction, cell division, apoptosis, and immune response. Ubiquitination is also named “lysine ubiquitination” because it occurs when an ubiquitin is covalently attached to lysine (K) residues of targeting proteins. Given an uncharacterized protein sequence that contains many lysine residues, which one of them is the ubiquitination site, and which one is of non-ubiquitination site? With the avalanche of protein sequences generated in the postgenomic age, it is highly desired for both basic research and drug development to develop an automated method for rapidly and accurately annotating the ubiquitination sites in proteins. In view of this, a new predictor called “iUbiq-Lys” was developed based on the evolutionary information, gray system model, as well as the general form of pseudo-amino acid composition. It was demonstrated via the rigorous cross-validations that the new predictor remarkably outperformed all its counterparts. As a web-server, iUbiq-Lys is accessible to the public at http://www.jci-bioinfo.cn/iUbiq-Lys. For the convenience of most experimental scientists, we have further provided a protocol of step-by-step guide, by which users can easily get their desired results without the need to follow the complicated mathematics that were presented in this paper just for the integrity of its development process.

Keywords:

• ubiquitination
• Chou’s PseAAC
• gray system model
• SVM
• web-server
• iUbiq-Lys

Acknowledgment

The authors wish to express their gratitude to the two anonymous reviewers for their constructive comments, which were very helpful in strengthening the presentation of this study.

Additional information

Funding

Funding. This work was partially supported by the National Nature Science Foundation of China [grant number 61261027]; the Key Project of Chinese Ministry of Education [grant number 210116]; Natural Science Foundation of Jiangxi Province, China [grant number 20142BAB207013], [grant number 20122BAB201044]; the Foundation of Jiangxi Education Committee, China [grant number GJJ14651].