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

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...

You might also read

Related Articles

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

Sort by
Same author

AI-Driven Design of Miniproteins as Potential Allosteric Modulators.

Pharmaceuticals (Basel, Switzerland)·2026
Same author

Allosteric regulation of enzymatic catalysis by molecular crowding.

Communications chemistry·2026
Same author

Unifying Constraints Linking Protein Folding and Native Dynamics Decoded from AlphaFold.

Physical review letters·2026
Same author

Structural organization of HBV pgRNA genome driven by phase separation in capsid confinement.

Nature communications·2026
Same author

Effect of Additional Terminal Residues on the Folding and Unfolding Dynamics of Cold Shock Protein.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2025
Same author

Dynamic Pathway of Guanidine-III Riboswitch Folding Revealed by Single-Molecule FRET: Mg<sup>2+</sup>-Assisted Preorganization and Ligand-Induced Kinetic Trapping.

ACS chemical biology·2025

Related Experiment Video

Updated: May 12, 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

Computational design of class II MHC binding peptide with sequence-based evolution information.

Ying Cao1,2, Yuqing Li2,3, Weitong Ren2

  • 1Postgraduate Training Base Alliance, Wenzhou Medical University, Wenzhou, Zhejiang Province 325000, China.

Bioinformatics Advances
|May 11, 2026
PubMed
Summary

Designing artificial peptides for Major Histocompatibility Complex class II (MHCII) binding is crucial for vaccine development. A Transformer neural network approach using sequence-based evolutionary data successfully designed high-affinity artificial peptides.

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous &beta;2-Microglobulin
11:17

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

Published on: March 10, 2021

Related Experiment Videos

Last Updated: May 12, 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

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

Stability and Structure of Bat Major Histocompatibility Complex Class I with Heterologous &beta;2-Microglobulin
11:17

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

Published on: March 10, 2021

Area of Science:

  • Immunology and computational biology
  • Molecular modeling and drug design

Background:

  • Major Histocompatibility Complex class II (MHCII)-peptide binding is essential for adaptive immunity, initiating T cell responses.
  • Designing artificial MHCII-binding peptides is vital for vaccine development but challenging due to peptide flexibility.

Purpose of the Study:

  • To develop a novel computational method for designing artificial MHCII-binding peptides.
  • To leverage sequence-based evolutionary information and advanced structure prediction for peptide design.

Main Methods:

  • Trained a Transformer neural network using sequence-based evolutionary data from native peptides.
  • Incorporated amino acid frequency distributions and joint frequency distributions from multiple sequence alignments.
  • Utilized an accurate sequence-based scoring function and AlphaFold3 for structure prediction.

Main Results:

  • Designed artificial peptides predicted to have binding affinities comparable to native peptides.
  • Achieved high structural confidence (pLDDT > 90.0) for designed peptides bound to MHCII.
  • Demonstrated the potential of sequence-based methods for functional peptide design.

Conclusions:

  • Established a novel paradigm for designing functional peptides using AI and sequence-based data.
  • The developed method offers significant assistance for biomedical researchers in vaccine development and other fields.
  • Highlights the power of integrating evolutionary information with deep learning for peptide design.