Proteasomal cleavage detection software tools | Immune system data analysis
Proteasomes, major proteolytic sites in eukaryotic cells, play an important part in major histocompatibility class I (MHC I) ligand generation and thus in the regulation of specific immune responses. Their cleavage specificity is of outstanding interest for this process.
Produces neural network predictions for cleavage sites of the human proteasome. NetChop has been trained on human data only, and will therefore presumably have better performance for prediction of the cleavage sites of the human proteasome. However, since the proteasome structure is quite conserved, we believe that the server is able to produce reliable predictions for at least the other mammalian proteasomes.
A bioinformatics tool for the prediction of potential antigenic epitopes presented on the cell surface by major histocompatibility complex class I (MHC I) molecules to CD8 positive T lymphocytes. MAPPP combines existing predictions for proteasomal cleavage with peptide anchoring to MHC I molecules. For calculating the cleavage probability of a specific fragment, we first determine the probability of a cut after each of the residues within the sequence. By limiting the minimum probability for a single residue in the form, one can limit the number of resulting possibilities. After that, a cleavage probability for all possible fragments between two cut-sites and with the right length is calculated. The cleavage probability for a fragment depends on the probability of either the N- and the C-residue, as well as the probabilities of the residues between these sites. The flanking regions to the left and the right of a fragment and the probabilities of their residues are considered too.
A prediction tool for cleavages by human and yeast proteasomes, based on experimental cleavage data. PAProC is particularly useful for immunologists working on antigen processing and the prediction of major histocompatibility complex class I molecule (MHC I) ligands and cytotoxic T-lymphocyte (CTL) epitopes. Likewise, in cases in which proteasomal protein degradation has been indicated in disease, PAProC can be used to assess the general cleavability of disease-linked proteins.
A support vector machine based method for the prediction of constitutive as well as immunoproteasome cleavage sites in antigenic sequences. Pcleavage achieved Matthew's correlation coefficents of 0.54 and 0.43 on in vitro and major histocompatibility complex ligand data, respectively. This shows that the performance of our method is comparable to that of the NetChop method, which is currently considered to be the best method for proteasome cleavage site prediction.
Predicts cleavage sites of the constitutive proteasome and the immunoproteasome. PCPS is a web server that allows the prediction of proteasome and immunoproteasome cleavage through N-gram models. The software executes the predictions on user-provided input data and returns the results to the browser. The proteasome models were built upon MHCI-eluted peptides whereas the immunoproteasome models were built upon CD8 T cell epitopes.
Allows the description of kinetics of specific protein fragments generated by 20S proteasomes in different conditions. ProteaMAlg is a model that aims to improve the analysis and predictions of the products and their kinetics of in vitro proteasome degradation. The software can quantitatively describe the in vitro digestion patterns of substrates with relatively simple dynamics. It was tested on several published data sets of in vitro degradations performed by 20S constitutive- or immunoproteasome.