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

Flexible ligand docking with Glide.

Matthew P Repasky1, Mee Shelley, Richard A Friesner

  • 1Schrodinger, L.L.C., New York, New York, USA.

Current Protocols in Bioinformatics
|April 23, 2008
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

A functional investigation of antibody Fc-FcRn variant binding guided by <i>in silico</i> free energy perturbation methods.

bioRxiv : the preprint server for biology·2026
Same author

Results of a Large-Scale Study of the Binding of 50 Type II Inhibitors to 348 Kinases: The Role of Protein Reorganization.

Journal of medicinal chemistry·2026
Same author

Evaluating Multiconfigurational Trials for Accurate Phaseless Auxiliary-Field Quantum Monte Carlo on 3d Transition Metal Complexes.

Journal of chemical theory and computation·2026
Same author

An Accurate Charge-Aware Machine-Learning Interatomic Potential for the Reduction of Li-Ion Battery Electrolytes in Solution.

Journal of chemical theory and computation·2026
Same author

Results of a large scale study of the binding of 50 type II inhibitors to 348 kinases: The role of protein reorganization.

bioRxiv : the preprint server for biology·2026
Same author

Glide WS: Methodology and Initial Assessment of Performance for Docking Accuracy and Virtual Screening.

Journal of chemical theory and computation·2025
Same journal

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.

Current protocols in bioinformatics·2020
Same journal

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.

Current protocols in bioinformatics·2020
Same journal

Network Building with the Cytoscape BioGateway App Explained in Five Use Cases.

Current protocols in bioinformatics·2020
Same journal

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.

Current protocols in bioinformatics·2020
Same journal

Exploring Non-Coding RNAs in RNAcentral.

Current protocols in bioinformatics·2020
Same journal

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource.

Current protocols in bioinformatics·2020
See all related articles

Glide is a powerful ligand docking program used for predicting protein-ligand interactions and screening compounds. It employs SP and XP GlideScore functions for ranking, offering flexible docking with optional constraints for accurate binding mode prediction.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Accurate prediction of protein-ligand binding is crucial for drug discovery.
  • Virtual screening methods are essential for identifying potential drug candidates.
  • Computational tools are needed to efficiently analyze molecular interactions.

Purpose of the Study:

  • To present protocols for flexible ligand docking using the Glide program.
  • To detail methods for predicting protein-ligand binding modes.
  • To explain ligand ranking strategies in high-throughput virtual screening.

Main Methods:

  • Utilizing the Glide ligand docking program.
  • Employing SP and XP GlideScore scoring functions for compound ranking.

Related Experiment Videos

  • Implementing three modes for sampling ligand conformational and positional flexibility.
  • Optionally incorporating ligand constraints or molecular similarity calculations.

    • Main Results:

    • Glide enables prediction of optimal ligand orientation relative to protein receptors.
    • The program facilitates high-throughput virtual screening of chemical libraries.
    • Scoring functions (SP and XP GlideScore) provide ranked lists of potential binders.

    Conclusions:

    • Glide is an effective tool for flexible ligand docking and virtual screening.
    • The program aids in identifying and ranking potential drug candidates based on predicted binding modes.
    • Protocols presented allow for customized docking strategies, including constraints and similarity searches.