ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives

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Abstract

Motivation:

Numerous ubiquitination sites remain undiscovered because of the limitations of mass spectrometry-based methods. Existing prediction methods use randomly selected non-validated sites as non-ubiquitination sites to train ubiquitination site prediction models.

Results:

We propose an evolutionary screening algorithm (ESA) to select effective negatives among non-validated sites and an ESA-based prediction method, ESA-UbiSite, to identify human ubiquitination sites. The ESA selects non-validated sites least likely to be ubiquitination sites as training negatives. Moreover, the ESA and ESA-UbiSite use a set of well-selected physicochemical properties together with a support vector machine for accurate prediction. Experimental results show that ESA-UbiSite with effective negatives achieved 0.92 test accuracy and a Matthews's correlation coefficient of 0.48, better than existing prediction methods. The ESA increased ESA-UbiSite's test accuracy from 0.75 to 0.92 and can improve other post-translational modification site prediction methods.

Availability and Implementation:

An ESA-UbiSite-based web server has been established at http://iclab.life.nctu.edu.tw/iclab_webtools/ESAUbiSite/.

Contact:

syho@mail.nctu.edu.tw

Supplementary information:

Supplementary data are available at Bioinformatics online.

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