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

Optimal docking area: a new method for predicting protein-protein interaction sites.

Juan Fernandez-Recio1, Max Totrov, Constantin Skorodumov

  • 1Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.

Proteins
|October 21, 2004
PubMed
Summary

We developed Optimal Docking Area (ODA), a new method to identify protein interaction sites. ODA accurately predicts protein-protein binding regions by analyzing surface energy, aiding structural biology research.

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

Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities.

bioRxiv : the preprint server for biology·2026
Same author

A Polypharmacology-Driven Approach to Alzheimer's Disease and Tauopathies: Rational Design, Synthesis and Characterization of Amino-Pyrazole-Based Multikinase (GSK-3β/FYN-α/DYRK1A) Inhibitors.

Journal of medicinal chemistry·2026
Same author

Menthol's disruptive effects on kanamycin-resistant Escherichia coli energy metabolism and ion fluxes.

Biophysical reports·2025
Same author

Modeling Protein-Protein Complexes by Combining pyDock and AlphaFold.

Methods in molecular biology (Clifton, N.J.)·2025
Same author

The multimerization pathway of the glucocorticoid receptor.

Nucleic acids research·2025
Same author

Performance of pyDock in 8th CAPRI: Energy-Based Scoring Applied to Docking and AlphaFold Models.

Proteins·2025

Area of Science:

  • Structural biology
  • Computational biology
  • Biophysics

Background:

  • Protein-protein association is crucial in biology, but predicting interaction sites is challenging.
  • Desolvation is a key factor in protein association, with hydrophobic interfaces common in obligate complexes.
  • Identifying interaction sites in non-obligate complexes requires advanced analytical methods.

Purpose of the Study:

  • To present Optimal Docking Area (ODA), a novel computational method for identifying protein-protein interaction sites.
  • To analyze protein surfaces for regions with favorable energy changes upon complex formation.
  • To validate the ODA method on diverse non-obligate protein-protein complexes.

Main Methods:

  • Developed the Optimal Docking Area (ODA) method to analyze protein surfaces.

Related Experiment Videos

  • Identified continuous surface patches with optimal docking desolvation energy.
  • Utilized atomic solvation parameters adjusted for protein-protein docking.
  • Validated ODA on 66 unbound structures of non-homologous proteins in non-obligate hetero-complexes.

    • Main Results:

    • Optimal docking areas with low surface energy were identified in approximately half of the tested proteins.
    • ODA correctly located 'hot spots' in known protein-protein binding sites in 80% of cases.
    • The method demonstrates accuracy in predicting binding regions from unbound structures.

    Conclusions:

    • The ODA method provides a fast and accurate approach for predicting protein-protein interaction sites.
    • Burial of low-surface-energy regions identified by ODA may drive the formation of encounter complexes.
    • ODA has potential applications in structural proteomics and understanding complex formation mechanisms.