Any tools for predicting binding affinity between TCR and epitode?
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3.9 years ago
CY ▴ 640

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?

TCR cancer tool prediction • 3.1k views
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3.6 years ago
niuyw ▴ 40

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.
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3.9 years ago
igor 12k

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.

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I believe that IEDB predicts MHC - epitope binding. Not epitope - TCR binding which is the next step once the epitope got presented to the cell surface.

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Thanks for clarifying.

IEDB has a lot of different tools, so I assumed they covered the full range. Maybe not.

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