I am working on a immunotherapy related project that identify tumor epitode (neiantigen) and TCR-seq. Say I already have both epitode and sequences of T/B cell CDR3 region available. Is there any tools available for predicting their binding affinity?
Hi! I found these tools by Google, but I haven't try any of them. Hope to be helpful.
- OncoPeptVAC: a robust TCR binding algorithm to prioritize neoepitope using tumor mutation (DNAseq) and gene expression (RNAseq) data.
- TCRex: a webtool for the prediction of T-cell receptor sequence epitope specificity.
- NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks.
- Repitope: epitope immunogenicity prediction through in silico TCR-peptide contact potential profiling.
I am not too familiar with this type of analysis, but IEDB Analysis Resource may be what you are looking for:
Welcome to the Immune Epitope Database Analysis Resource. This site provides a collection of tools for the prediction and analysis of immune epitopes. It serves as a companion site to the Immune Epitope Database (IEDB) , a manually curated database of experimentally characterized immune epitopes.