T cell epitope prediction and its application to immunotherapy

AL Schaap-Johansen, M Vujović, A Borch… - Frontiers in …, 2021 - frontiersin.org
T cells play a crucial role in controlling and driving the immune response with their ability to
discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we …

Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants

R Yin, BY Feng, A Varshney, BG Pierce - Protein Science, 2022 - Wiley Online Library
High‐resolution experimental structural determination of protein–protein interactions has led
to valuable mechanistic insights, yet due to the massive number of interactions and …

TCRmodel2: high-resolution modeling of T cell receptor recognition using deep learning

R Yin, HV Ribeiro-Filho, V Lin… - Nucleic Acids …, 2023 - academic.oup.com
The cellular immune system, which is a critical component of human immunity, uses T cell
receptors (TCRs) to recognize antigenic proteins in the form of peptides presented by major …

Methods for sequence and structural analysis of B and T cell receptor repertoires

S Teraguchi, DS Saputri… - Computational and …, 2020 - Elsevier
B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of
defense molecules that, collectively, can distinguish self from non-self and facilitate …

H3K27M neoepitope vaccination in diffuse midline glioma induces B and T cell responses across diverse HLA loci of a recovered patient

T Boschert, K Kromer, T Lerner, K Lindner… - Science …, 2024 - science.org
H3K27M, a driver mutation with T and B cell neoepitope characteristics, defines an
aggressive subtype of diffuse glioma with poor survival. We functionally dissect the immune …

Comparative analysis of the CDR loops of antigen receptors

WK Wong, J Leem, CM Deane - Frontiers in immunology, 2019 - frontiersin.org
The adaptive immune system uses two main types of antigen receptors: T-cell receptors
(TCRs) and antibodies. While both proteins share a globally similar β-sandwich architecture …

CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases

AF Fonseca, DA Antunes - Frontiers in Immunology, 2023 - frontiersin.org
T-cell-based immunotherapies hold tremendous potential in the fight against cancer, thanks
to their capacity to specifically targeting diseased cells. Nevertheless, this potential has been …

Predicting T cell receptor antigen specificity from structural features derived from homology models of receptor-peptide-major histocompatibility complexes

M Milighetti, J Shawe-Taylor, B Chain - Frontiers in Physiology, 2021 - frontiersin.org
The physical interaction between the T cell receptor (TCR) and its cognate antigen causes T
cells to activate and participate in the immune response. Understanding this physical …

[HTML][HTML] Strengths and limitations of web servers for the modeling of TCRpMHC complexes

HN Le, MV de Freitas, DA Antunes - Computational and Structural …, 2024 - Elsevier
Cellular immunity relies on the ability of a T-cell receptor (TCR) to recognize a peptide (p)
presented by a class I major histocompatibility complex (MHC) receptor on the surface of a …

Cracking the code of adaptive immunity: The role of computational tools

K Vegesana, PG Thomas - Cell Systems, 2024 - cell.com
In recent years, the advances in high-throughput and deep sequencing have generated a
diverse amount of adaptive immune repertoire data. This surge in data has seen a …