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A neural network based MHC Class-I Binding Peptide Prediction Server
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This section of the server will provide complete information to users about the method. how users can use the server in prediction of MHC binders or CTL epitopes ?.what is the performence of method.The description of various step or aspects of the prediction is as follows:-

A sample of the submission form showing appropriate places for submitting sequence and varying other measures for running prediction.

  1. Threshold :-The varation in the threshold will result a varation in the stringency of the prediction. As the server shows the thresold in value like 1%,2% so on. The threshold of 1% predict peptides in any given protein sequence which belong to the 1% best scoring natural peptides. The threshold correlate with the peptide score and therefore with HLA-ligand interaction. More importantly, threshold is an indicator of the likelihood that predicted peptide is capable of binding to a given HLA-molecule.Lower the threshold (= high stringency), lower the false positive rate and the higher the false negative rate.In contrast higher the threshold (= low stringency), higher the false positive rate and lower the false negative rate. In short, from the same protein sequence input, a threshold setting of 1% will predict a lower number of peptide sequences and for a lower number of HLA-II alleles, compared to 2% or higher thresholds; however, this will also ensure a higher likelihood of positive downstream experimental results. Normally, at least for a first round of screening, threshold values higher than 3% are not desirable, since the rate of false positives can increase the size of the predicted repertoire to an amount unacceptable for later experimental testing.

  2. Proteasome AND Immunoproteasome Filters:-The proteasome play a critical role in deciding which of MHC binder act as CTL epitope.The testing of peptides binding to MHC is indispensible. But there still remain the possibilty that these peptides are not generated in vivo by proteasome.So , it is possible to narrow down the number of CTL epitopes by including the proteasomal preferences in MHC prediction. Here we have used the standard or/and immuno proteasome matrices to refine the MHC binders to CTL epitopes.The matrices are derived from the work of Toe et al.,2002.These matrices consider the 12 amino acid peptide and make a cleavage at center position that is six amino acids away from N-terminal.The user can vary the stringency of locating the proteasomal cleavage site by varying the threshold. The higher the value of threshold non-stringent will be the prediction.The lower is the value of threshold more stringent will be the prediction.The threshold values are calculated in similar manner as for quantitative matrices.

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