[HTML][HTML] A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach

P Wang, J Sidney, C Dow, B Mothé… - PLoS computational …, 2008 - journals.plos.org
The identification of MHC class II restricted peptide epitopes is an important goal in
immunological research. A number of computational tools have been developed for this …

Improved methods for predicting peptide binding affinity to MHC class II molecules

KK Jensen, M Andreatta, P Marcatili, S Buus… - …, 2018 - Wiley Online Library
Major histocompatibility complex class II (MHC‐II) molecules are expressed on the surface
of professional antigen‐presenting cells where they display peptides to T helper cells, which …

[HTML][HTML] A community resource benchmarking predictions of peptide binding to MHC-I molecules

B Peters, HH Bui, S Frankild, M Nielsen… - PLoS computational …, 2006 - journals.plos.org
Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules
by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a …

Automated benchmarking of peptide-MHC class I binding predictions

T Trolle, IG Metushi, JA Greenbaum, Y Kim… - …, 2015 - academic.oup.com
Motivation: Numerous in silico methods predicting peptide binding to major
histocompatibility complex (MHC) class I molecules have been developed over the last …

[HTML][HTML] Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior

Y Kim, J Sidney, C Pinilla, A Sette, B Peters - BMC bioinformatics, 2009 - Springer
Background Experts in peptide: MHC binding studies are often able to estimate the impact of
a single residue substitution based on a heuristic understanding of amino acid similarity in …

An automated benchmarking platform for MHC class II binding prediction methods

M Andreatta, T Trolle, Z Yan, JA Greenbaum… - …, 2018 - academic.oup.com
Motivation Computational methods for the prediction of peptide-MHC binding have become
an integral and essential component for candidate selection in experimental T cell epitope …

[HTML][HTML] Prediction of MHC class I binding peptides, using SVMHC

P Dönnes, A Elofsson - BMC bioinformatics, 2002 - Springer
Background T-cells are key players in regulating a specific immune response. Activation of
cytotoxic T-cells requires recognition of specific peptides bound to Major Histocompatibility …

NetMHCpan-4.0: improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data

V Jurtz, S Paul, M Andreatta, P Marcatili… - The Journal of …, 2017 - journals.aai.org
Cytotoxic T cells are of central importance in the immune system's response to disease.
They recognize defective cells by binding to peptides presented on the cell surface by MHC …

[HTML][HTML] Dataset size and composition impact the reliability of performance benchmarks for peptide-MHC binding predictions

Y Kim, J Sidney, S Buus, A Sette, M Nielsen… - BMC bioinformatics, 2014 - Springer
Background It is important to accurately determine the performance of peptide: MHC binding
predictions, as this enables users to compare and choose between different prediction …

[HTML][HTML] Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes

W Zhao, X Sher - PLoS computational biology, 2018 - journals.plos.org
A number of machine learning-based predictors have been developed for identifying
immunogenic T-cell epitopes based on major histocompatibility complex (MHC) class I and II …