T Cell Epitope Prediction Tools
T Cell Epitopes - MHC Binding PredictionThese tools predict IC50 values for peptides binding to specific MHC molecules. Note that binding to MHC is necessary but not sufficient for recognition by T cells.
This tool will take in an amino acid sequence, or set of sequences and determine each subsequence's ability to bind to a specific MHC class I molecule.
This tool employs different methods to predict MHC Class II epitopes, including a consensus approach which combines NN-align, SMM-align and Combinatorial library methods.
The Tepitool provides prediction of peptides binding to MHC class I and class II molecules. Tool is designed as a wizard with 6 steps as described below. Each field (except sequences and alleles) is filled with default recommended settings for prediction and selection of optimum peptides. The input parameters can be adjusted as per your specific needs. You can go back to previous steps to change your selection before submission of the job. Once you submit the job (at the end of step-6), you will not be able to make any more changes and will have to start the prediction all over again with updated input parameters.
T Cell Epitopes - Processing PredictionThese tools predict epitope candidates based upon the processing of peptides in the cell.
This tool combines predictors of proteasomal processing, TAP transport, and MHC binding to produce an overall score for each peptide's intrinsic potential of being a T cell epitope.
Neural network based prediction of proteasomal cleavage sites (NetChop) and T cell epitopes (NetCTL and NetCTLpan)
NetChop is a predictor of proteasomal processing based upon a neural network. NetCTL and NetCTLpan are predictors of T cell epitopes along a protein sequence. It also employs a neural network architecture.
MHC-NP employs data obtained from MHC elution experiments in order to assess the probability that a given peptide is naturally processed and binds to a given MHC molecule. This tool was the winner of the 2nd Machine Learning Competition in Immunology.
This tool utilizes MHC II ligand elution data to predict naturally processed MHC II ligands by scanning the given peptide sequences.
T Cell Epitopes - Immunogenicity PredictionThis tool predicts the relative ability of a peptide/MHC complex to elicit an immune response.
This tool uses amino acid properties as well as their position within the peptide to predict the immunogenicity of a class I peptide MHC (pMHC) complex.
The deimmunization tool is attempt to identify immunodominant regions in a given therapeutically important protein, and suggest amino-acid substitutions that create non-immunogenic versions of the proteins. So we have opted a two steps process; 1) In the first step, the deimmunization tool will list all the immunogenic regions or peptides based on selected threshold. These peptides will be generated from the protein with 15mer window size and 10mer overlap. 2) In the second step, the user can select one or more peptides listed in the results and final result window will display the non-immunogenic substitution of each selected peptides. The default threshold is 8.5 (which is difference in the median of percentile rank from 26 reference alleles set for MHC class II). In the final result window, the tools will also take care of the fact that non-immunogenic substitution in the immunogenic peptides, should not create new immunogenic site in the neighboring peptides. Therefore, the result window will also display the effect of substitution on the neighboring peptides.
The server is developed to predict the allele independent CD4 T cell immunogenicity at population level. User can predict the T cell immunogenicity using 7-allele method (Paul et. al. 2015), immunogenicity method and combined method (IEDB recommended). The combined method predicts the final score that combines the predictions from 7-allele method and immunogenicity method.
TCRMatch compares input CDR3b sequences against curated CDR3b sequences in the IEDB to find matches that are predicted to share epitope specificity. Matches are determined by sequence similarity, which is scored using a comprehensive k-mer comparison.
The LYRA server predicts structures for either T-Cell Receptors (TCR) or B-Cell Receptors (BCR) using homology modelling. Framework templates are selected based on BLOSUM score, and complementary determining regions (CDR) are then selected if needed based on a canonical structure model and grafted onto the framework templates.
SCEptRe provides weekly updated, non-redundant, user customized benchmark datasets with information on the immune receptor features for receptor-specific epitope predictions. This tool extracts weekly updated 3D complexes of antibody-antigen, TCR-pMHC and MHC-ligand from the Immune Epitope Database (IEDB) and clusters them based on antigens, receptors and epitopes to generate benchmark datasets. Users can customize structural quality and clustering parameters (e.g. resolution, R free factors, antigen or epitope sequence identity) to generate these datasets based on their need.
DockTope is a web-based tool, based on D1-EM-D2 approach, intended to allow the pMHC-I modeling. This tool has been developed by Gustavo Fioravanti Vieira's group and has been deployed to the IEDB-AR servers with minimal modification by the IEDB team.
: Tools under AR Labs which are experimental and are not quite ready for production yet. They are intended for further research, updates and testing.