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

New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen

P H Walls1, M J Sternberg

  • 1Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, Lincoln's Inn Fields, London, U.K.

Journal of Molecular Biology
|November 5, 1992
PubMed
Summary

This study introduces a new algorithm for modeling protein-protein interactions, specifically antibody-antigen docking, using surface complementarity. The method accurately predicts docking orientations with deviations under 4.8 Å, even using predicted antibody structures.

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

Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM.

Proteins·2002
Same author

Generating protein three-dimensional fold signatures using inductive logic programming.

Computers & chemistry·2002
Same author

PML bodies associate specifically with the MHC gene cluster in interphase nuclei.

Journal of cell science·2001
Same author

A structural census of metabolic networks for E. coli.

Journal of molecular biology·2001
Same author

Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.

Journal of molecular biology·2001
Same author

An approach to improving multiple alignments of protein sequences using predicted secondary structure.

Protein engineering·2001

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Protein-protein interactions are crucial for biological processes.
  • Accurate modeling of these interactions, particularly antibody-antigen docking, is essential for drug discovery and understanding immune responses.
  • Existing methods often struggle with flexibility and computational cost.

Purpose of the Study:

  • To develop and validate a novel algorithm for modeling protein-protein interactions, focusing on antibody-antigen docking.
  • To assess the algorithm's accuracy and efficiency in predicting docking orientations.
  • To explore the use of predicted antibody structures in docking studies.

Main Methods:

  • A novel algorithm modeling protein-protein interactions via surface complementarity.

Related Experiment Videos

  • Utilizes a soft potential for steric scoring, allowing for structural flexibility during docking.
  • Incorporates a simple electrostatic model to filter infeasible interactions.
  • Employs biochemical knowledge (epitope residues, distance constraints) to refine docking results.
  • Implemented on a single instruction/multiple datastream (SI/MD) parallel architecture computer.

    • Main Results:

    • The algorithm successfully modeled four antibody-lysozyme complexes, including one using a predicted antibody structure.
    • Identified 15-40 possible docking orientations per system.
    • Achieved root-mean-square (r.m.s.) deviations between 1.9 Å and 4.8 Å in the interface region for all modeled complexes.
    • Demonstrated efficient search of the conformational space within a two-day search time on the parallel architecture.

    Conclusions:

    • The novel algorithm effectively models antibody-antigen docking using surface complementarity and flexibility.
    • The method provides accurate predictions, even with predicted antibody structures.
    • The use of a parallel architecture ensures comprehensive search and reasonable computation time, making it a valuable tool for structural biology research.