Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14740%2F24%3A00139165" target="_blank" >RIV/00216224:14740/24:00139165 - isvavai.cz</a>

Result on the web

<a href="https://www.nature.com/articles/s43588-024-00653-0" target="_blank" >https://www.nature.com/articles/s43588-024-00653-0</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1038/s43588-024-00653-0" target="_blank" >10.1038/s43588-024-00653-0</a>

Result language

angličtina

Original language name

Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen

Original language description

T cell receptor (TCR) recognition of foreign peptides presented by major histocompatibility complex protein is a major event in triggering the adaptive immune response to pathogens or cancer. The prediction of TCR-peptide interactions has great importance for therapy of cancer as well as infectious and autoimmune diseases but remains a major challenge, particularly for novel (unseen) peptide epitopes. Here we present TCRen, a structure-based method for ranking candidate unseen epitopes for a given TCR. The first stage of the TCRen pipeline is modeling of the TCR-peptide-major histocompatibility complex structure. Then a TCR-peptide residue contact map is extracted from this structure and used to rank all candidate epitopes on the basis of an interaction score with the target TCR. Scoring is performed using an energy potential derived from the statistics of TCR-peptide contact preferences in existing crystal structures. We show that TCRen has high performance in discriminating cognate versus unrelated peptides and can facilitate the identification of cancer neoepitopes recognized by tumor-infiltrating lymphocytes.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

—

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2024

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

NATURE COMPUTATIONAL SCIENCE

ISSN

2662-8457

e-ISSN

2662-8457

Volume of the periodical

4

Issue of the periodical within the volume

7

Country of publishing house

GB - UNITED KINGDOM

Number of pages

15

Pages from-to

1-15

UT code for WoS article

001268935300002

EID of the result in the Scopus database

2-s2.0-85198063639