Related Experiment Video

Updated: Jul 5, 2026

A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
07:59

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

Published on: March 25, 2014

Support vector machine-based prediction of MHC-binding peptides

Pierre Dönnes1

  • 1Division for Simulation of Biological Systems, Eberhard Karls University Tübingen, Germany. pierre.doennes@roche.com

Methods in Molecular Biology (Clifton, N.J.)
|May 3, 2008
PubMed

The use of major histocompatibility complex (MHC) class I binding peptides for immunotherapeutic purposes has shown promising results in recent years. The identification of such peptides mostly starts with predicting MHC-binding peptides, given a protein of interest. An accurate prediction method can reduce the number of peptides that needs to be tested experimentally. This protocol describes in this describes how support vector machines (SVMs) can be used for predicting MHC class I binding peptides. Focus is given on data representation, the concept of cross-validation, and how optimal SVM-specific parameters are obtained.

More Related Videos

Immunopeptidomics: Isolation of Mouse and Human MHC Class I- and II-Associated Peptides for Mass Spectrometry Analysis09:32

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

Published on: October 15, 2021

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Related Concept Videos

Conserved Binding Sites01:49

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...
Antigens Involved in Adaptive Immunity01:26

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.
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...