The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding
Motivation: Receptor–ligand interactions play an important role in controlling many
biological systems. One prominent example is the binding of peptides to the major …
biological systems. One prominent example is the binding of peptides to the major …
NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets
M Nielsen, M Andreatta - Genome medicine, 2016 - Springer
Background Binding of peptides to MHC class I molecules (MHC-I) is essential for antigen
presentation to cytotoxic T-cells. Results Here, we demonstrate how a simple alignment step …
presentation to cytotoxic T-cells. Results Here, we demonstrate how a simple alignment step …
Pan-specific MHC class I predictors: a benchmark of HLA class I pan-specific prediction methods
H Zhang, C Lundegaard, M Nielsen - Bioinformatics, 2009 - academic.oup.com
Motivation: MHC: peptide binding plays a central role in activating the immune surveillance.
Computational approaches to determine T-cell epitopes restricted to any given major …
Computational approaches to determine T-cell epitopes restricted to any given major …
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools
L Zhang, K Udaka, H Mamitsuka… - Briefings in …, 2012 - academic.oup.com
Binding of short antigenic peptides to major histocompatibility complex (MHC) molecules is
a core step in adaptive immune response. Precise identification of MHC-restricted peptides …
a core step in adaptive immune response. Precise identification of MHC-restricted peptides …
NNAlign: a platform to construct and evaluate artificial neural network models of receptor–ligand interactions
M Nielsen, M Andreatta - Nucleic acids research, 2017 - academic.oup.com
Peptides are extensively used to characterize functional or (linear) structural aspects of
receptor–ligand interactions in biological systems, eg SH2, SH3, PDZ peptide-recognition …
receptor–ligand interactions in biological systems, eg SH2, SH3, PDZ peptide-recognition …
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior
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 …
a single residue substitution based on a heuristic understanding of amino acid similarity in …
Structure-based methods for binding mode and binding affinity prediction for peptide-MHC complexes
Understanding the mechanisms involved in the activation of an immune response is
essential to many fields in human health, including vaccine development and personalized …
essential to many fields in human health, including vaccine development and personalized …
Predicting Class II MHC-Peptide binding: a kernel based approach using similarity scores
J Salomon, DR Flower - BMC bioinformatics, 2006 - Springer
Background Modelling the interaction between potentially antigenic peptides and Major
Histocompatibility Complex (MHC) molecules is a key step in identifying potential T-cell …
Histocompatibility Complex (MHC) molecules is a key step in identifying potential T-cell …
Automated benchmarking of peptide-MHC class I binding predictions
Motivation: Numerous in silico methods predicting peptide binding to major
histocompatibility complex (MHC) class I molecules have been developed over the last …
histocompatibility complex (MHC) class I molecules have been developed over the last …
Prediction of peptide-MHC binding using profiles
PA Reche, EL Reinherz - Immunoinformatics: predicting immunogenicity in …, 2007 - Springer
Prediction of peptide binding to major histocompatibility complex (MHC) molecules is a
basis for anticipating T-cell epitopes. Peptides that bind to a given MHC molecule are …
basis for anticipating T-cell epitopes. Peptides that bind to a given MHC molecule are …