Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Comparison of extracellular vesicle isolation methods reveals method-dependent protein and miRNA profiles in saliva.

Extracellular vesicles and circulating nucleic acids·2026
Same author

Natural history of antiplatelet antibody formation in patients with Glanzmann thrombasthenia: a French multicenter prospective study.

Journal of thrombosis and haemostasis : JTH·2026
Same author

Capturing Emotions Induced by Fragrances in Saliva: Objective Emotional Assessment Based on Molecular Biomarker Profiles.

Biosensors·2026
Same author

Corrigendum to "PepLess: A computational tool developed to optimize SPOT synthesis and analyze related immunoassay data" [J. Biochem. Biophys. Rep. 44, (December 2025), 102301].

Biochemistry and biophysics reports·2026
Same author

PepLess: A computational tool developed to optimize SPOT synthesis and analyze related immunoassay data.

Biochemistry and biophysics reports·2025
Same author

AtSnRK2.4 Functions as an ABA-Responsive Protein Kinase in Arabidopsis.

Physiologia plantarum·2025

Related Experiment Video

Updated: Dec 31, 2025

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

15.5K

Benchmarking the PEPOP methods for mimicking discontinuous epitopes.

Vincent Demolombe1, Alexandre G de Brevern2,3,4,5, Franck Molina6

  • 1BPMP, CNRS, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.

BMC Bioinformatics
|January 1, 2020
PubMed
Summary

The improved PEPOP version 2.0 offers 32 new methods for predicting peptides that mimic discontinuous epitopes, outperforming previous tools and chance. Optimized PEPOP methods effectively identify peptides matching true epitopes.

Keywords:
Antigen-antibody interactionAntigenicityBenchmarkingDiscontinuous B-cell epitopeImmunogenicityMolecular mimicryPeptide designProtein surfaceProtein-protein interactions (PPI)Structural bioinformatics

More Related Videos

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope
08:09

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope

Published on: March 24, 2017

9.9K
Peptide:MHC Tetramer-based Enrichment of Epitope-specific T cells
13:58

Peptide:MHC Tetramer-based Enrichment of Epitope-specific T cells

Published on: October 22, 2012

18.5K

Related Experiment Videos

Last Updated: Dec 31, 2025

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

15.5K
Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope
08:09

Peptide Scanning-assisted Identification of a Monoclonal Antibody-recognized Linear B-cell Epitope

Published on: March 24, 2017

9.9K
Peptide:MHC Tetramer-based Enrichment of Epitope-specific T cells
13:58

Peptide:MHC Tetramer-based Enrichment of Epitope-specific T cells

Published on: October 22, 2012

18.5K

Area of Science:

  • Computational biology
  • Immunoinformatics
  • Structural biology

Background:

  • Computational methods aid in identifying protein epitopes for biomarker discovery.
  • PEPOP version 1.0 was an initial tool for antigenic/immunogenic peptide prediction.
  • PEPOP version 2.0 enhances epitope prediction with new methods for discontinuous epitopes.

Purpose of the Study:

  • To introduce and evaluate 32 new peptide prediction methods in PEPOP version 2.0.
  • To guide the selection of peptides mimicking discontinuous epitopes.
  • To assess the performance of these novel methods in predicting epitopes.

Main Methods:

  • Benchmarking involved comparing predicted peptides against experimentally determined epitopes from 75 antigen-antibody complexes.
  • Performance was assessed using Sensitivity (Se) and Positive Predictive Value (PPV).
  • Results were compared against random predictions and the SUPERFICIAL tool.

Main Results:

  • 33 out of 34 PEPOP methods demonstrated superior performance compared to the SUPERFICIAL tool.
  • PEPOP methods were found to be more efficient than random peptide prediction.
  • Optimized PEPOP methods showed the highest accuracy in matching predicted peptides to true epitopes.

Conclusions:

  • PEPOP version 2.0 significantly improves peptide epitope prediction capabilities.
  • The new methods provide a valuable tool for identifying peptides that mimic discontinuous epitopes.
  • Optimized PEPOP methods are effective for designing peptides that accurately represent protein epitopes.