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 Experiment Videos

Knowledge-based grouping of modeled HLA peptide complexes.

P Kangueane1, M K Sakharkar, K S Lim

  • 1BioInformatics Centre, National University of Singapore, Singapore, Singapore. kangs@bic.nus.edu.sg

Human Immunology
|April 25, 2000
PubMed
Summary
This summary is machine-generated.

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

Inclusive Search for Anomalous Single-Photon Production in MicroBooNE.

Physical review letters·2026
Same author

Artificial intelligence-powered automatic tooth segmentation from cone-beam computed tomography for the fabrication of surgical splints.

International journal of oral and maxillofacial surgery·2026
Same author

First Search for Dark Sector e^{+}e^{-} Explanations of the MiniBooNE Anomaly at MicroBooNE.

Physical review letters·2026
Same author

Determinants and long-term outcomes of treatment delays in young and middle-aged acute ischemic stroke patients: a prospective cohort study.

BMC neurology·2026
Same author

First Measurement of Charged-Current Muon-Neutrino-Induced K^{+} Production on Argon Using the MicroBooNE Detector.

Physical review letters·2026
Same author

Search for an Anomalous Production of Charged-Current ν_{e} Interactions without Visible Pions across Multiple Kinematic Observables in MicroBooNE.

Physical review letters·2025

Predicting which peptides bind to human leukocyte antigens (HLA) is challenging due to gene polymorphism. This study introduces a modeling approach using van der Waals clashes and solvent-exposed hydrophobic residues to accurately identify peptide binders.

Area of Science:

  • Immunogenetics
  • Computational Biology
  • Structural Biology

Background:

  • Human leukocyte antigens (HLA) are highly polymorphic genes crucial for immune response.
  • Polymorphisms in peptide-binding domains complicate the prediction of HLA-peptide interactions.
  • Existing computational methods for predicting peptide binding have limitations, particularly regarding data availability for specific HLA alleles.

Purpose of the Study:

  • To develop and validate a computational modeling scheme for predicting peptides that bind to specific HLA molecules.
  • To assess the effectiveness of knowledge-based rules, specifically van der Waals clashes and solvent-exposed hydrophobic residues, in discriminating binders from non-binders.

Main Methods:

  • Utilized a modeling scheme to create HLA-peptide complexes.

Related Experiment Videos

  • Applied knowledge-based rules focusing on the number of atomic clashes (vdWC) and solvent-exposed hydrophobic peptide residues (SEHPR) to score these complexes.
  • Compared predicted binding scores with experimental binding data.

    • Main Results:

    • The scoring scheme effectively discriminated known binders from non-binders.
    • Solved crystal complexes showed a high frequency of no van der Waals clashes (95%) and no solvent-exposed hydrophobic peptide residues (86%).
    • The method correctly grouped 77% of peptides as good binders with 71% sensitivity when compared against experimental data.

    Conclusions:

    • A computational modeling approach incorporating rules for van der Waals clashes and solvent-exposed hydrophobic residues is a promising tool for predicting HLA-peptide binding.
    • This method offers an alternative to knowledge-based prediction methods when allele-specific binding data is scarce.
    • The validated scoring scheme aids in the selection of peptides for specific HLA molecules, relevant for immunological studies and therapeutic development.