pSuc-PseRat: Predicting Lysine Succinylation in Proteins by Exploiting the Ratios of Sequence Coupling and Properties

Abstract

Abstract

Lysine succinylation is an extremely important protein post-translational modification that plays a fundamental role in regulating various biological reactions, and dysfunction of this process is associated with a number of diseases. Thus, determining which Lys residues in an uncharacterized protein sequence are succinylated underpins both basic research and drug development endeavors. To solve this problem, we have developed a predictor called pSuc-PseRat. The features of the pSuc-PseRat predictor are derived from two aspects: (1) the binary encoding from succinylated sites and non-succinylated sites; (2) the sequence-coupling effects between succinylated sites and non-succinylated sites. Eleven gradient boosting machine classifiers were trained with these features to build the predictor. The pSuc-PseRat predictor achieved an average ACU (area under the receiver operating characteristic curve) score of 0.805 in the fivefold cross-validation set and performed better than existing predictors on two comprehensive independent test sets. A freely available web server has been developed for pSuc-PseRat.