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 …

MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules

KR Govindarajan, P Kangueane, TW Tan… - …, 2003 - academic.oup.com
Binding of short antigenic peptides to Major histocompatibility complex (MHC) proteins is the
first step in T-cell mediated immune response. To understand the structural principles …

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 …

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 …

Predicting peptide binding to Major Histocompatibility Complex molecules

WWP Liao, JW Arthur - Autoimmunity reviews, 2011 - Elsevier
The Major Histocompatibility Complex (MHC) constitutes an important part of the human
immune system. During infection, pathogenic proteins are processed into peptide fragments …

Rosetta FlexPepDock to predict peptide-MHC binding: An approach for non-canonical amino acids

N Bloodworth, NR Barbaro, R Moretti, DG Harrison… - PloS one, 2022 - journals.plos.org
Computation methods that predict the binding of peptides to MHC-I are important tools for
screening and identifying immunogenic antigens and have the potential to accelerate …

Ab initio prediction of peptide‐MHC binding geometry for diverse class I MHC allotypes

AJ Bordner, R Abagyan - Proteins: Structure, Function, and …, 2006 - Wiley Online Library
Since determining the crystallographic structure of all peptide‐MHC complexes is infeasible,
an accurate prediction of the conformation is a critical computational problem. These models …

Predicting the affinity of peptides to major histocompatibility complex class II by scoring molecular dynamics simulations

R Ochoa, A Laio, P Cossio - Journal of Chemical Information and …, 2019 - ACS Publications
Predicting the binding affinity of peptides able to interact with major histocompatibility
complex (MHC) molecules is a priority for researchers working in the identification of novel …

Predicting peptide binding to MHC pockets via molecular modeling, implicit solvation, and global optimization

HD Schafroth, CA Floudas - Proteins: Structure, Function, and …, 2004 - Wiley Online Library
Abstract Development of a computational prediction method based on molecular modeling,
global optimization, and implicit solvation has produced accurate structure and relative …

Rapid, precise, and reproducible prediction of peptide–MHC binding affinities from molecular dynamics that correlate well with experiment

S Wan, B Knapp, DW Wright, CM Deane… - Journal of chemical …, 2015 - ACS Publications
The presentation of potentially pathogenic peptides by major histocompatibility complex
(MHC) molecules is one of the most important processes in adaptive immune defense …