Carbonylation site detection software tools | Post-translational modification data analysis
Protein carbonylation is one of the most pervasive oxidative stress-induced post-translational modifications (PTMs), which plays a significant role in the etiology and progression of several human diseases. It has been regarded as a biomarker of oxidative stress due to its relatively early formation and stability compared with other oxidative PTMs.
It could be used to identify carbonylation sites of query human protein sequences. CarSPred consists of four modules which are devoted to K, R, T and P carbonylation site prediction separately. It receives protein sequences or file in FASTA format as input. For output result, list and file are optional and the annotations will clearly indicate the precise location and probability of putative carbonylation site in the sequence.
Identifies carbonylation sites in human proteins. CarSite predicts carbonylation sites by position-specific amino acid propensity feature extraction in combination with the composition of k-spaced amino acid pairs, amino acid composition and the composition of hydrophobic and hydrophilic amino acids feature extractions.
Addresses the problem of the carbonylation identification for an uncharacterized protein sequence containing many residues of K, P, R, or T. iCar-PseCp incorporates the sequence-coupled information into the general pseudo amino acid composition, and balances out skewed training dataset by Monte Carlo sampling to expand positive subset. The approach can also be used to analyze many other problems in computational proteomics.
Predicts protein carbonylation sites. PredCar-site incorporates the sequence-coupled information in the general pseudo amino acid composition. It is designed by using a support vector machine (SVM) to classify carbonylation sites. The tool is able to dealing with real data and selects the values of parameters considering highest performance which will be measured using a specific metric. PredCar-site can be useful in drug development.