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

A multivariate approach to investigate docking parameters' effects on docking performance.

C David Andersson1, Elin Thysell, Anton Lindström

  • 1Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.

Journal of Chemical Information and Modeling
|June 15, 2007
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

Analysis of ligand recognition by choline O-acetyltransferase reveals thiol-reactive assay interference and weak ligand affinity in solution.

The Journal of biological chemistry·2026
Same author

Morphological heterogeneities in prostate cancer bone metastases are related to molecular subtypes and prognosis.

Clinical & experimental metastasis·2025
Same author

The Molecular Properties of Honey Bee Acetylcholinesterase Reveal Opportunities to Avoid Off-Target Effects in Insecticide Discovery.

Chemistry (Weinheim an der Bergstrasse, Germany)·2025
Same author

Tolerogenic antigen-specific vaccine induces VISTA-enriched regulatory T cells and protects against arthritis in DRB1∗04:01 mice.

Molecular therapy : the journal of the American Society of Gene Therapy·2025
Same author

Corneal Graft Rejection: Is It Reflected in Peripheral Immune Cells? Results of a Prospective Multicenter Study (VISICORT).

Transplantation·2024
Same author

A PSA SNP associates with cellular function and clinical outcome in men with prostate cancer.

Nature communications·2024
Same journal

Mapping Evolution of Molecules across Biochemistry with Assembly Theory.

Journal of chemical information and modeling·2026
Same journal

Structural Proteomics-Based Deciphering of Hydrophobic Packing Fingerprints Informing Protein Thermostability in TIM Barrels.

Journal of chemical information and modeling·2026
Same journal

Bridging between Structure-Based and Data-Driven Affinity Prediction.

Journal of chemical information and modeling·2026
Same journal

Reinforcement Learning-Driven Multiproperty Optimization in Molecular Design Using Multicontext Transcriptome Data.

Journal of chemical information and modeling·2026
Same journal

EnsembleCycPerm: Interpretable Modeling of Cyclic Peptide Permeability through Solvent-Dependent Conformational Ensembles.

Journal of chemical information and modeling·2026
Same journal

Resolving Conformational Preferences of Monosaccharides from <sup>1</sup>H and <sup>13</sup>C NMR Chemical Shifts Using an Integrated MD and QM Approach.

Journal of chemical information and modeling·2026
See all related articles

Optimizing docking software parameters like FRED and GOLD is crucial for drug discovery. Statistical analysis reveals specific settings significantly improve protein-ligand interaction predictions, enhancing accuracy for diverse protein targets.

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • Protein-ligand docking software is vital for drug discovery.
  • Parameter settings significantly influence docking accuracy.
  • Default parameters are often suboptimal, despite known improvements with expert tuning.

Purpose of the Study:

  • To systematically analyze the impact of docking parameters on performance.
  • To identify optimal parameter settings for FRED and GOLD software.
  • To investigate parameter influence across diverse protein-ligand complexes.

Main Methods:

  • Utilized statistical experimental design and regression analysis.
  • Employed partial least squares projections to latent structures (PLS) modeling.

Related Experiment Videos

  • Selected diverse protein-ligand complexes from the PDBbind database using principal component analysis.

    • Main Results:

    • Established quantitative relationships between docking parameters and accuracy.
    • Identified key parameters and their optimal settings for FRED and GOLD.
    • Demonstrated significant variation in results based on parameter settings and protein complexes.

    Conclusions:

    • Parameter optimization holds great potential for improving docking performance.
    • Tailoring settings to specific protein-ligand sets can enhance predictive accuracy.
    • This study provides a framework for optimizing docking software parameters in drug discovery.