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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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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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

Prediction of peptide-MHC binding using profiles.

Pedro A Reche1, Ellis L Reinherz

  • 1Department of Immunology, Faculated de Medicina, Universidad Complutense de Madrid, Madrid, 28040,Spain. parecheg@med.ucm.es

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

Predicting peptide binding to major histocompatibility complex (MHC) molecules is key for identifying T-cell epitopes. This study details using position-specific scoring matrices (PSSMs) to accurately predict peptide-MHC binding and T-cell epitopes.

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

Published on: January 26, 2024

Area of Science:

  • Immunology
  • Computational Biology
  • Bioinformatics

Background:

  • Predicting peptide binding to major histocompatibility complex (MHC) molecules is crucial for identifying T-cell epitopes.
  • Peptide binding to MHC molecules is influenced by sequence similarity.

Purpose of the Study:

  • To describe a method for deriving alignments and position-specific scoring matrices (PSSMs) for predicting peptide-MHC binding.
  • To utilize PSSMs as predictors of peptide-MHC binding and T-cell epitopes.

Main Methods:

  • Deriving sequence alignments from known peptide-MHC binders.
  • Constructing position-specific scoring matrices (PSSMs) from these alignments.
  • Comparing query peptide sequences to PSSMs to assess binding potential.

Main Results:

  • Developed a method to derive alignments and PSSMs suitable for peptide-MHC binding prediction.
  • Demonstrated that PSSMs can effectively predict peptide-MHC binding and T-cell epitopes based on sequence similarity.

Conclusions:

  • Position-specific scoring matrices (PSSMs) are valuable tools for predicting peptide-MHC binding.
  • This approach aids in the identification of T-cell epitopes, with implications for vaccine design and immunotherapy.