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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...

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Related Experiment Video

Updated: Jun 23, 2025

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes

Published on: March 25, 2014

In Silico Tools for Predicting Novel Epitopes.

Carolina Barra¹, Jonas Birkelund Nilsson², Astrid Saksager²

¹Section for Bioinformatics, Health Tech, Technical University of Denmark, Lyngby, Denmark. carolet@dtu.dk.

Methods in Molecular Biology (Clifton, N.J.)

|June 18, 2024

Summary

This summary is machine-generated.

Identifying pathogen antigens is crucial for vaccine development and understanding host immune responses. This work reviews experimental and in silico methods for predicting T cell and B cell epitopes, aiding in accelerated discovery.

Keywords:

B cell epitopes Epitope prediction Immunogenicity predictionImmunogenicity prediction MHC presentation T cell epitopes

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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

Area of Science:

Immunology
Computational Biology
Vaccinology

Background:

Antigen identification is vital for developing vaccines and diagnostics.
Historically, experimental methods identified immunogenic pathogen fragments.
This data informed rules of epitope and immunogenicity, leading to predictive tools.

Purpose of the Study:

To introduce basic concepts of MHC presentation and epitope identification.
To review experimental methods for determining epitopes.
To focus on state-of-the-art in silico epitope prediction methods, including their strengths and limitations.

Main Methods:

Review of experimental techniques for antigen and epitope discovery.
Discussion of in silico tools for predicting T cell and B cell epitopes.
Analysis of the strengths and limitations of current prediction methodologies.

Main Results:

Abundant data exists on immunogenic pathogen fragments.
Development of numerous in silico tools for epitope prediction.
These tools accelerate the identification of novel epitopes, reducing experimental costs.

Conclusions:

Epitope prediction tools are essential for modern immunology and vaccine design.
Understanding MHC presentation and epitope properties is key.
Rational use of prediction tools enhances biomedical research efficiency.