Question: Any tools for predicting binding affinity between TCR and epitode?
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gravatar for CY
2.7 years ago by
CY560
United States
CY560 wrote:

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?

cancer tool prediction tcr • 2.3k views
ADD COMMENTlink modified 2.4 years ago by niuyw30 • written 2.7 years ago by CY560
1
gravatar for niuyw
2.4 years ago by
niuyw30
China/Beijing
niuyw30 wrote:

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.
ADD COMMENTlink written 2.4 years ago by niuyw30
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gravatar for igor
2.7 years ago by
igor12k
United States
igor12k wrote:

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.

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by igor12k

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.

ADD REPLYlink written 2.7 years ago by CY560

Thanks for clarifying.

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

ADD REPLYlink written 2.7 years ago by igor12k
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