Structural Prediction of Peptide–MHC Binding Modes

MAS Perez, MA Cuendet, UF Röhrig… - … Science: Methods and …, 2022 - Springer
The immune system is constantly protecting its host from the invasion of pathogens and the
development of cancer cells. The specific CD8+ T-cell immune response against virus …

Structure-based methods for binding mode and binding affinity prediction for peptide-MHC complexes

DA Antunes, JR Abella, D Devaurs… - Current topics in …, 2018 - ingentaconnect.com
Understanding the mechanisms involved in the activation of an immune response is
essential to many fields in human health, including vaccine development and personalized …

A practical guide to structure-based prediction of MHC-binding peptides

S Ranganathan, JC Tong - Immunoinformatics: Predicting Immunogenicity …, 2007 - Springer
The binding of bound peptide ligands to major histocompatibility complex (MHC) molecules
plays a key role in the activation of normal immune responses and is an intricate theoretical …

[HTML][HTML] General prediction of peptide-MHC binding modes using incremental docking: a proof of concept

DA Antunes, D Devaurs, M Moll, G Lizée, LE Kavraki - Scientific reports, 2018 - nature.com
The class I major histocompatibility complex (MHC) is capable of binding peptides derived
from intracellular proteins and displaying them at the cell surface. The recognition of these …

[HTML][HTML] Towards universal structure-based prediction of class II MHC epitopes for diverse allotypes

AJ Bordner - PLoS One, 2010 - journals.plos.org
The binding of peptide fragments of antigens to class II MHC proteins is a crucial step in
initiating a helper T cell immune response. The discovery of these peptide epitopes is …

[HTML][HTML] Accurate modeling of peptide-MHC structures with AlphaFold

V Mikhaylov, CA Brambley, GLJ Keller, AG Arbuiso… - Structure, 2024 - cell.com
Major histocompatibility complex (MHC) proteins present peptides on the cell surface for T
cell surveillance. Reliable in silico prediction of which peptides would be presented and …

GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking

HH Kyeong, Y Choi, HS Kim - Bioinformatics, 2018 - academic.oup.com
Motivation The identification of T-cell epitopes has many profound translational applications
in the areas of transplantation, disease diagnosis, vaccine/therapeutic protein development …

Predicting TCR-peptide recognition based on residue-level pairwise statistical potential

VK Karnaukhov, DS Shcherbinin, AO Chugunov… - bioRxiv, 2022 - biorxiv.org
T cell receptor (TCR) recognition of foreign peptides presented by major histocompatibility
complex (MHC) proteins is a crucial step in triggering the adaptive immune response …

[HTML][HTML] Physicochemical heuristics for identifying high fidelity, near-native structural models of Peptide/MHC complexes

GLJ Keller, LI Weiss, BM Baker - Frontiers in Immunology, 2022 - frontiersin.org
There is long-standing interest in accurately modeling the structural features of peptides
bound and presented by class I MHC proteins. This interest has grown with the advent of …

APE-Gen2. 0: Expanding Rapid Class I Peptide–Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide …

R Fasoulis, MM Rigo, G Lizée… - Journal of Chemical …, 2024 - ACS Publications
The recognition of peptides bound to class I major histocompatibility complex (MHC-I)
receptors by T-cell receptors (TCRs) is a determinant of triggering the adaptive immune …