T cell epitope predictions

B Peters, M Nielsen, A Sette - Annual Review of Immunology, 2020 - annualreviews.org
Throughout the body, T cells monitor MHC-bound ligands expressed on the surface of
essentially all cell types. MHC ligands that trigger a T cell immune response are referred to …

The pockets guide to HLA class I molecules

AT Nguyen, C Szeto, S Gras - Biochemical Society Transactions, 2021 - portlandpress.com
Human leukocyte antigens (HLA) are cell-surface proteins that present peptides to T cells.
These peptides are bound within the peptide binding cleft of HLA, and together as a …

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 …

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 …

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] 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 …

MHC class II epitope predictive algorithms

M Nielsen, O Lund, S Buus, C Lundegaard - Immunology, 2010 - Wiley Online Library
Major histocompatibility complex class II (MHC‐II) molecules sample peptides from the
extracellular space, allowing the immune system to detect the presence of foreign microbes …

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 …

Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens

F Guarra, G Colombo - Journal of Chemical Theory and …, 2023 - ACS Publications
The design of new biomolecules able to harness immune mechanisms for the treatment of
diseases is a prime challenge for computational and simulative approaches. For instance, in …

[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 …