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PAProC / Prediction Algorithm for Proteasomal Cleavages
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.
MAPPP / MHC-I Antigenic Peptide Processing Prediction
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.
ProteaMAlg / Proteasome Modeling Algorithm
Obsolete
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.
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