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Antigens Involved in Adaptive Immunity

Antigens Involved in Adaptive Immunity

An antigen is any substance the immune system identifies as foreign and potentially harmful to the body, prompting an immune response. Antigens have two functional properties: immunogenicity and reactivity. Immunogenicity is the ability of an antigen to stimulate a specific immune response. At the same time, reactivity describes the antigen's ability to react with the cells and antibodies produced in response to it.
Complete Antigens
Complete antigens possess both immunogenicity and reactivity.

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jun 28, 2026

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

Published on: October 15, 2021

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

Ilka Hoof¹, Bjoern Peters, John Sidney

¹Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Building 208, 2800, Lyngby, Denmark. ilka@cbs.dtu.dk

|November 13, 2008

Summary

NetMHCpan-2.0 accurately predicts peptide binding to diverse major histocompatibility complex (MHC) class I molecules, including uncharacterized human leukocyte antigen (HLA) alleles and non-human primate variants. This tool aids immunologists in understanding cellular immune responses and pathogen recognition.

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Last Updated: Jun 28, 2026

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis

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Published on: October 15, 2021

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Published on: March 25, 2014

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β2-Microglobulin

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous β₂-Microglobulin

Published on: March 10, 2021

Area of Science:

Immunology
Bioinformatics
Computational Biology

Background:

Peptide binding to major histocompatibility complex (MHC) molecules is crucial for cellular immune system pathogen recognition.
The human leukocyte antigen (HLA) region is highly polymorphic, with many MHC alleles and their specificities uncharacterized.
Limited experimental characterization exists for chimpanzee and rhesus macaque MHC class I molecules.

Purpose of the Study:

To present NetMHCpan-2.0, a computational method for predicting peptide-MHC class I binding affinities.
To validate NetMHCpan-2.0's accuracy across a wide range of human and non-human primate MHC alleles.
To demonstrate the utility of NetMHCpan-2.0 in interpreting immune responses and guiding immunological research.

Main Methods:

Trained NetMHCpan-2.0 on an extensive dataset of quantitative MHC binding affinities.
Included data from human (HLA-A, HLA-B), chimpanzee, rhesus macaque, gorilla, and mouse MHC class I molecules.
Evaluated prediction accuracy for uncharacterized HLA molecules (e.g., HLA-C, HLA-G) and non-human primate MHCs.

Main Results:

NetMHCpan-2.0 accurately predicts binding affinities for uncharacterized human HLA molecules.
The method demonstrates high accuracy for chimpanzee and rhesus macaque MHC class I molecules.
Successfully predicted high-affinity binding peptides for pig SLA-1*0401, with 93% binding stronger than 500 nM.

Conclusions:

NetMHCpan-2.0 provides robust quantitative predictions for diverse peptide-MHC class I interactions.
The tool's broad allelic coverage extends beyond human MHC molecules, including non-human primates.
NetMHCpan-2.0 is a valuable resource for immunologists studying cellular immune responses in various species.