Question: Any tools for predicting binding affinity between TCR and epitode?
gravatar for CY
2.7 years ago by
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
gravatar for niuyw
2.4 years ago by
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
gravatar for igor
2.7 years ago by
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
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1309 users visited in the last hour