A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

S Mei, F Li, A Leier, TT Marquez-Lago… - Briefings in …, 2020 - academic.oup.com
Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility
complex (MHC) class I loci in humans. The binding and interaction between HLA-I …

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 …

NetMHCpan, a Method for Quantitative Predictions of Peptide Binding to Any HLA-A and -B Locus Protein of Known Sequence

M Nielsen, C Lundegaard, T Blicher, K Lamberth… - PloS one, 2007 - journals.plos.org
Background Binding of peptides to Major Histocompatibility Complex (MHC) molecules is
the single most selective step in the recognition of pathogens by the cellular immune system …

Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research

HH Lin, GL Zhang, S Tongchusak, EL Reinherz… - BMC …, 2008 - Springer
Background Initiation and regulation of immune responses in humans involves recognition
of peptides presented by human leukocyte antigen class II (HLA-II) molecules. These …

DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility

I Antes - Proteins: Structure, Function, and Bioinformatics, 2010 - Wiley Online Library
Molecular docking programs play an important role in drug development and many well‐
established methods exist. However, there are two situations for which the performance of …

[HTML][HTML] Deimmunization of protein therapeutics–Recent advances in experimental and computational epitope prediction and deletion

LV Zinsli, N Stierlin, MJ Loessner… - Computational and …, 2021 - Elsevier
Biotherapeutics, and antimicrobial proteins in particular, are of increasing interest for human
medicine. An important challenge in the development of such therapeutics is their potential …

Fully blind peptide-protein docking with pepATTRACT

CEM Schindler, SJ de Vries, M Zacharias - Structure, 2015 - cell.com
Peptide-protein interactions are ubiquitous in the cell and form an important part of the
interactome. Computational docking methods can complement experimental …

Accurate prediction of DnaK-peptide binding via homology modelling and experimental data

J Van Durme, S Maurer-Stroh, R Gallardo… - PLoS computational …, 2009 - journals.plos.org
Molecular chaperones are essential elements of the protein quality control machinery that
governs translocation and folding of nascent polypeptides, refolding and degradation of …

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 …

HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes

S Gupta, S Nerli, S Kutti Kandy, GL Mersky… - Nature …, 2023 - nature.com
The class I proteins of the major histocompatibility complex (MHC-I) display epitopic
peptides derived from endogenous proteins on the cell surface for immune surveillance …