Fundamentals and methods for T‐and B‐cell epitope prediction

JL Sanchez-Trincado… - Journal of …, 2017 - Wiley Online Library
Adaptive immunity is mediated by T‐and B‐cells, which are immune cells capable of
developing pathogen‐specific memory that confers immunological protection. Memory and …

[HTML][HTML] Immunoinformatics and epitope prediction in the age of genomic medicine

L Backert, O Kohlbacher - Genome medicine, 2015 - Springer
Immunoinformatics involves the application of computational methods to immunological
problems. Prediction of B-and T-cell epitopes has long been the focus of immunoinformatics …

NetMHCpan, a method for MHC class I binding prediction beyond humans

I Hoof, B Peters, J Sidney, LE Pedersen, A Sette… - Immunogenetics, 2009 - Springer
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. The human …

NetMHCcons: a consensus method for the major histocompatibility complex class I predictions

E Karosiene, C Lundegaard, O Lund, M Nielsen - Immunogenetics, 2012 - Springer
A key role in cell-mediated immunity is dedicated to the major histocompatibility complex
(MHC) molecules that bind peptides for presentation on the cell surface. Several in silico …

[HTML][HTML] Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

B Peters, A Sette - BMC bioinformatics, 2005 - Springer
Background Many processes in molecular biology involve the recognition of short
sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major …

The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC-peptide binding

H Zhang, O Lund, M Nielsen - Bioinformatics, 2009 - academic.oup.com
Motivation: Receptor–ligand interactions play an important role in controlling many
biological systems. One prominent example is the binding of peptides to the major …

Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers

C Lundegaard, O Lund, M Nielsen - Bioinformatics, 2008 - academic.oup.com
Several accurate prediction systems have been developed for prediction of class I major
histocompatibility complex (MHC): peptide binding. Most of these are trained on binding …

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 …

[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 …

[HTML][HTML] Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research

HH Lin, S Ray, S Tongchusak, EL Reinherz, V Brusic - BMC immunology, 2008 - Springer
Background Protein antigens and their specific epitopes are formulation targets for epitope-
based vaccines. A number of prediction servers are available for identification of peptides …