Additional file 1: of Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction

Performance of the Success predictor using 6-, 8- and 10-fold cross-validation. (DOCX 148 kb

Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams

<div><p>Post-translational modification refers to the biological mechanism involved in the enzymatic modification of proteins after being translated in the ribosome. This mechanism comprises a wide range of structural modifications, which bring dramatic variations to the biological function of proteins. One of the recently discovered modifications is succinylation. Although succinylation can be detected through mass spectrometry, its current experimental detection turns out to be a timely process unable to meet the exponential growth of sequenced proteins. Therefore, the implementation of fast and accurate computational methods has emerged as a feasible solution. This paper proposes a novel classification approach, which effectively incorporates the secondary structure and evolutionary information of proteins through profile bigrams for succinylation prediction. The proposed predictor, abbreviated as SSEvol-Suc, made use of the above features for training an AdaBoost classifier and consequently predicting succinylated lysine residues. When SSEvol-Suc was compared with four benchmark predictors, it outperformed them in metrics such as sensitivity (0.909), accuracy (0.875) and Matthews correlation coefficient (0.75).</p></div

Additional file 2: of Success: evolutionary and structural properties of amino acids prove effective for succinylation site prediction

Numbers of succinylation sites detected by each predictor. (XLS 119 kb

Comparison of SSEvol-Suc and state-of-the-art predictors.

<p>Comparison of SSEvol-Suc and state-of-the-art predictors.</p

Schematic representation of a lysine residue and its surrounding amino acids.

<p>(A) lysine with 15 residues on both sides, (B) lysine with missing residues to the right and left.</p

Improving succinylation prediction accuracy by incorporating the secondary structure via helix, strand and coil, and evolutionary information from profile bigrams - Fig 2

<p>Receiver operating characteristic of SSEvol-Suc for (A) 6-, (B) 8- and (C) 10-fold cross-validations.</p

Additional file 1: of Oasis 2: improved online analysis of small RNA-seq data

Oasis2-Suppl-Material.docx: This file contains supplementary material and figures as well. (DOCX 125 kb