T-cell epitope vaccine design by immunoinformatics

A Patronov, I Doytchinova - Open biology, 2013 - royalsocietypublishing.org
Vaccination is generally considered to be the most effective method of preventing infectious
diseases. All vaccinations work by presenting a foreign antigen to the immune system in …

An introduction to epitope prediction methods and software

X Yang, X Yu - Reviews in medical virology, 2009 - Wiley Online Library
In this paper, current prediction methods and algorithms for both T‐and B cell epitopes are
reviewed, and a comprehensive summary of epitope prediction software and databases …

Structure based prediction of neoantigen immunogenicity

TP Riley, GLJ Keller, AR Smith, LM Davancaze… - Frontiers in …, 2019 - frontiersin.org
The development of immunological therapies that incorporate peptide antigens presented to
T cells by MHC proteins is a long sought-after goal, particularly for cancer, where mutated …

[HTML][HTML] Two complementary methods for predicting peptides binding major histocompatibility complex molecules

K Gulukota, J Sidney, A Sette, C DeLisi - Journal of molecular biology, 1997 - Elsevier
Peptides that bind to major histocompatibility complex products (MHC) are known to exhibit
certain sequence motifs which, though common, are neither necessary nor sufficient for …

Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins

D Rognan, SL Lauemøller, A Holm… - Journal of medicinal …, 1999 - ACS Publications
A simple and fast free energy scoring function (Fresno) has been developed to predict the
binding free energy of peptides to class I major histocompatibility (MHC) proteins. It differs …

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 …

Toward the quantitative prediction of T-cell epitopes: coMFA and coMSIA studies of peptides with affinity for the class I MHC molecule HLA-A* 0201

IA Doytchinova, DR Flower - Journal of medicinal chemistry, 2001 - ACS Publications
A set of 102 peptides with affinity for the class I MHC HLA-A* 0201 molecule was subjected
to three-dimensional quantitative structure− affinity relationship (3D QSAR) studies using …

Methods and protocols for prediction of immunogenic epitopes

JC Tong, TW Tan, S Ranganathan - Briefings in Bioinformatics, 2007 - academic.oup.com
T-cell recognition of peptide/major histocompatibility complex (MHC) is a prerequisite for
cellular immunity. Recently, there has been an influx of bioinformatics tools to facilitate the …

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 …

JenPep: a novel computational information resource for immunobiology and vaccinology

H McSparron, MJ Blythe, C Zygouri… - Journal of chemical …, 2003 - ACS Publications
JenPep is a relational database containing a compendium of thermodynamic binding data
for the interaction of peptides with a range of important immunological molecules: the major …