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

Protein docking for low-resolution structures

I A Vakser1

  • 1Center for Molecular Design, Washington University, St Louis, MO 63130, USA.

Protein Engineering
|April 1, 1995
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

How common is the funnel-like energy landscape in protein-protein interactions?

Protein science : a publication of the Protein Society·2001
Same author

Residue frequencies and pairing preferences at protein-protein interfaces.

Proteins·2001
Same author

Side chains in transmembrane helices are shorter at helix-helix interfaces.

Proteins·2000
Same author

A systematic study of low-resolution recognition in protein--protein complexes.

Proceedings of the National Academy of Sciences of the United States of America·1999
Same author

Identification of the binding site on cytochrome P450 2B4 for cytochrome b5 and cytochrome P450 reductase.

The Journal of biological chemistry·1998
Same author

Construction of a 3D model of cytochrome P450 2B4.

Protein engineering·1997
Same journal

Structure of a human Rhinovirus complexed with its receptor molecule.

Protein engineering·2024
Same journal

pH-responsive polymer-assisted refolding of urea- and organic solvent-denatured alpha-chymotrypsin.

Protein engineering·2004
Same journal

Evaluation of different linker regions for multimerization and coupling chemistry for immobilization of a proteinaceous affinity ligand.

Protein engineering·2004
Same journal

Recombinant porcine intestinal carboxylesterase: cloning from the pig liver esterase gene by site-directed mutagenesis, functional expression and characterization.

Protein engineering·2004
Same journal

Periplasmic expression of human growth hormone via plasmid vectors containing the lambdaPL promoter: use of HPLC for product quantification.

Protein engineering·2004
Same journal

Shift of fibril-forming ability of the designed alpha-helical coiled-coil peptides into the physiological pH region.

Protein engineering·2004
See all related articles

This study presents a novel molecular docking method that bypasses the need for highly accurate 3D structures. The approach successfully predicts complex configurations even with imprecise molecular data, aiding in molecular recognition.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Molecular docking is crucial for predicting complex configurations but is hindered by inaccuracies in 3D molecular structures.
  • Existing methods struggle with substantial conformational changes or poorly defined structures from sources like NMR or modeling.

Purpose of the Study:

  • To develop and validate a robust molecular docking procedure that accommodates imprecise or incomplete 3D structural data.
  • To enable accurate prediction of molecular complex configurations when detailed structural information is unavailable.

Main Methods:

  • A modified docking algorithm was employed, utilizing molecules with structural features no smaller than 7 Å.
  • The procedure was tested on various protein complexes from the Brookhaven Protein Data Bank.

Related Experiment Videos

Main Results:

  • The modified docking approach demonstrated a strong tendency to predict correct molecular complex structures.
  • Accurate prediction of real binding sites was achieved in most tested cases.
  • Differences in predicting antigen-antibody complexes suggest unique formation principles.

Conclusions:

  • The developed recognition procedure is effective for molecular docking studies lacking precise 3D structural data.
  • This method offers a viable solution for molecular recognition challenges posed by structural uncertainties.