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

Development and validation of a genetic algorithm for flexible docking

G Jones1, P Willett, R C Glen

  • 1Department of Information Studies and Krebs Institute for Biomolecular Research, University of Sheffield, Western Bank, UK.

Journal of Molecular Biology
|April 4, 1997
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

Prediction of biological activity for high-throughput screening using binary kernel discrimination.

Journal of chemical information and computer sciences·2001
Same author

Molecular complexity and its impact on the probability of finding leads for drug discovery.

Journal of chemical information and computer sciences·2001
Same author

Measuring blood volume with fluorescent-labeled hydroxyethyl starch.

Critical care medicine·2001
Same author

Synergy between combinatorial chemistry and de novo design.

Journal of molecular graphics & modelling·2001
Same author

Where are the GaPs? A rational approach to monomer acquisition and selection.

Journal of chemical information and computer sciences·2000
Same author

Molecular genetics improves the management of hereditary non-polyposis colorectal cancer.

South African medical journal = Suid-Afrikaanse tydskrif vir geneeskunde·2000
Same journal

UPF3A and UPF3B shape the transcriptome cooperatively yet oppose cell function.

Journal of molecular biology·2026
Same journal

Antibody-secreting cells integrate efficient NMD with non‑canonical UPR signaling to maintain proteostasis and support massive immunoglobulin synthesis.

Journal of molecular biology·2026
Same journal

Small molecule stabilization of diverse amyloidogenic immunoglobulin light chains revealed by hydrogen-deuterium exchange mass spectrometry.

Journal of molecular biology·2026
Same journal

UPF1 at Work: Structural and Mechanistic Insights Into a Master Regulator of Nonsense-Mediated mRNA Decay.

Journal of molecular biology·2026
Same journal

Structural basis for the pro-amyloidogenic action and ligand binding of a novel W72R variant of human apolipoprotein A-I.

Journal of molecular biology·2026
Same journal

Cryo-EM Structure of the C. elegans Septin Tetramer Reveals a Revised Architecture and Conserved Positional Orthology.

Journal of molecular biology·2026
See all related articles

The GOLD program accurately predicts small molecule binding modes to proteins, crucial for rational drug design. This genetic algorithm-based docking tool achieved a 71% success rate in identifying experimental binding poses.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Predicting small molecule binding modes to macromolecules is vital for rational drug design.
  • The "docking" problem requires accurate prediction of ligand-protein interactions.

Purpose of the Study:

  • To report the development and validation of the GOLD (Genetic Optimisation for Ligand Docking) program.
  • To enhance the reliability and applicability of automated ligand docking algorithms.

Main Methods:

  • Utilized a genetic algorithm to explore ligand conformational flexibility and partial protein flexibility.
  • Incorporated the displacement of loosely bound water molecules as a key binding requirement.
  • Tested the advanced algorithm on a dataset of 100 protein-ligand complexes from the Brookhaven Protein DataBank.

Related Experiment Videos

Main Results:

  • The GOLD program demonstrated a 71% success rate in identifying experimental binding modes when docking ligands back into their native binding sites.
  • Numerous enhancements to the original technique significantly improved the algorithm's reliability and applicability.

Conclusions:

  • The GOLD program represents a substantial advancement in automated ligand docking for rational drug design.
  • The validated algorithm provides a reliable tool for predicting small molecule binding modes, aiding in the discovery of new therapeutics.