NetChop is a predictor of proteasomal processing based upon a neural network. NetCTL is a predictor of T cell epitopes along a protein sequence. It also employs a neural network architecture. NetCTLpan is an update to the original NetCTL server that allows for prediction of CTL epitope with restriction to any MHC molecules of known protein sequence.

Step 1: Select either NetCHOP, NetCTL or NetCTLpan method.
Step 2: Either paste sequence(s) in FASTA format in the textarea shown, or click browse and submit a file in FASTA format.
Step 3: Depending on what method is selected, enter the parameters for the program or leave the default values.
The Step 4 for each individual methods and their expected results are given below.

• NetChop - produces neural network predictions for cleavage sites of the human proteasome.
• NetCTL - predicts CTL epitopes in protein sequences.
• NetCTLpan - is an update to the original NetCTL that allows for prediction of CTL epitope with restriction to any MHC molecules of known protein sequence.

Step 4: Click on submit.
The following shows the predicted continuous epitopes as a chart of NetChop score Vs. residue position. You can change the threshold for predictions, view results in table format, save the prediction result or start with a new prediction. The positive predictions are displayed in green, while the predictions below the threshold value are in red.
The table below shows the tabular view of NetChop prediction result. Again, the positive predictions are displayed in green font.

• # - residue position
• Amino Acid - Amino acid residue
• Prediction Score - NetChop prediction score

Step 4: Click on submit.
The chart below shows the predicted continuous epitopes of NetCTL score Vs. residue position. You can change the threshold for predictions, view results in table format, save the prediction result or start with a new prediction. The positive predictions are displayed in green, while the predictions below the threshold value are in red.
NetCTL table view lists following columns. The positive predictions are displayed in green.

• # - residue position
• Peptide Sequence - Amino acid residue
• Predicted MHC Binding Affinity - The value is given as 1 - log50k(aff), where log50k is the logarithm with base 50.000, and aff is the affinity in nM units
• Rescale Binding Affinity - The predicted binding affinity is normalized by the 1st percentile score
• C Terminal Cleavage Affinity - Predicted proteasomal cleavage score
• TAP Transport Efficiency - Predicted TAP transport efficiency
• Prediction Score - Overall prediction score

Addition options:
Frequently occurring alleles check-box:
By default "Show only frequently occurring alleles" check-box is checked. This allows the selection of only those alleles that occur in at least 1% of the human population or allele frequency of 1% or higher. However, un-checking the check-box will allow selection of all the alleles and corresponding peptide lengths for a particular species.

* Note that some of the HLA alleles are denoted with the supertype they represent, in parenthesis.

• Threshold for showing predictions: This threshold filters the combined prediction score and displays only those that are greater than the threshold.
• Weight on C terminal cleavage: Relative weight on proteasomal cleavage.
• Weight on TAP transport efficiency: Relative weight on TAP transport efficiency predicted using weight matrix based method describe by Peters et al., 2003.
• Threshold for epitope identification: Threshold for epitope identification is the threshold to label predictions a epitopes. This threshold is based on the %rank score.
• Percentile for positive prediction: Percentile cutoff value for positive prediction.

Step 4: Click on submit.
The chart below shows the predicted continuous epitopes of NetCTLpan score Vs. residue position. You can change the predictions percentile threshold, view results in table format, save the prediction result or start with a new prediction. The positive predictions are displayed in green, while the predictions below the threshold value are in red.
NetCTLpan table view lists following columns. The positive predictions are displayed in green.

• # - residue position
• MHC Prediction - MHC Prediction score (in 1-log50K(aff) uniqs)
• TAP Prediction score - Predicted TAP transport efficiency
• Cleavage Prediction score - Predicted proteasomal cleavage score
• Combined Prediction score - Overall prediction score
• %Rank - %Rank of prediction score to a set of 1000 random natural 9mer peptides