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

Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking

M Meyer1, P Wilson, D Schomburg

  • 1GBF (Gesellschaft für Biotechnologische Forschung) Abt., Molekulare Strukturforschung, Braunschweig, Germany.

Journal of Molecular Biology
|November 22, 1996
PubMed
Summary

A new geometric docking algorithm efficiently identifies protein binding sites by analyzing molecular surface complementarity and hydrogen bonding. This method reduces computational time and improves the accuracy of protein complex predictions.

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

The BRENDA enzyme information system-From a database to an expert system.

Journal of biotechnology·2017
Same author

BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation.

BMC bioinformatics·2010
Same author

Binding of inhibitory aromatic amino acids to Streptomyces griseus aminopeptidase.

Acta crystallographica. Section D, Biological crystallography·2004
Same author

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

Bioinformatics (Oxford, England)·2004
Same author

Dynamic generation and qualitative analysis of metabolic pathways by a joint database/graph theoretical approach.

Functional & integrative genomics·2003
Same author

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Bioinformatics (Oxford, England)·2002

Area of Science:

  • Computational Biology
  • Biochemistry
  • Structural Biology

Background:

  • Protein-protein interactions are crucial for biological processes.
  • Accurate prediction of protein complex structures is essential for understanding function and disease.
  • Existing docking algorithms face challenges in conformational search space and computational efficiency.

Purpose of the Study:

  • To develop and optimize a novel geometric docking algorithm for predicting protein complex structures.
  • To enhance computational efficiency by reducing the conformational search space.
  • To improve the accuracy of identifying geometrically complementary protein interfaces.

Main Methods:

  • Developed a geometric docking algorithm utilizing correlation analysis for protein molecular surface complementarity.

Related Experiment Videos

  • Implemented a physico-chemical pre-filter based on intermolecular hydrogen bond prediction to reduce conformational space.
  • Defined donor and acceptor sites based on atomic positions and van der Waals surface properties.
  • Utilized transformation invariant parameterization and refinement techniques (simplex method, correlation) for pose prediction.

    • Main Results:

    • Successfully reduced the conformational search space through a hydrogen bond-based pre-filter.
    • Demonstrated improved geometric ranking of predicted protein complex conformations.
    • Achieved a significant reduction in computational time (CPU time) for docking calculations.
    • Validated the algorithm's utility in identifying candidate docking conformations.

    Conclusions:

    • The developed geometric docking algorithm effectively quantifies molecular surface complementarity.
    • The hydrogen bond pre-filter significantly enhances computational efficiency and accuracy in protein docking.
    • The algorithm provides a reliable method for reducing conformational space and improving the ranking of protein complex structures.