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

Analysis and optimization of structure-based virtual screening protocols. (3). New methods and old problems in

Ryan Smith1, Roderick E Hubbard, Daniel A Gschwend

  • 1York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 4DD, UK.

Journal of Molecular Graphics & Modelling
|June 12, 2003
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

The impact of vitamins A and D on lung function and regulatory epigenetics in adult and childhood asthma.

Thorax·2026
Same author

Gastrointestinal Interoception and Relapse in Anorexia Nervosa.

JAMA psychiatry·2026
Same author

Structure-Based Discovery of Potent BCL-XL Inhibitors through Rescaffolding.

Journal of medicinal chemistry·2026
Same author

Genome sequencing identifies monogenic causes in adults with metabolic diseases.

Journal of the Endocrine Society·2026
Same author

Methylome-wide association study in blood suggests cell type-specific relationships between DNA methylation and lifetime anxiety.

Nature communications·2026
Same author

Semaglutide slows epigenetic aging in a randomized trial of HIV-associated lipohypertrophy.

Nature communications·2026
Same journal

Residue-level insights into SGLT2 inhibition and Nav1.5 selectivity of gliflozin derivatives: A molecular dynamics and pharmacophore-guided study.

Journal of molecular graphics & modelling·2026
Same journal

A benchmarking-informed structure-based virtual screening strategy targeting Lm-PTR1: Leveraging the Northern African natural products database.

Journal of molecular graphics & modelling·2026
Same journal

In Silico identification of natural and synthetic inhibitors targeting KRAS mutants (G12D, G12V, and G12C) and wild-type in pancreatic cancer.

Journal of molecular graphics & modelling·2026
Same journal

Structural evolution, mechanical and thermal stability of 7-40 mol% yttria-stabilized zirconia: First-principles investigation.

Journal of molecular graphics & modelling·2026
Same journal

Halide-encapsulated C<sub>24</sub> fullerenes as molecular redox hosts for alkali metals: A density functional theory study.

Journal of molecular graphics & modelling·2026
Same journal

Efficacy of Tinospora cordifolia bioactives as agonists of Smoothened (Smo) receptor to promote oligodendroglial lineage induction for remyelination-based therapy.

Journal of molecular graphics & modelling·2026
See all related articles

This study introduces a novel scoring function design for structure-based virtual screening (SVS). It combines crystallographic data with SVS calculation results, avoiding assay data and improving docking interaction recognition.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Structure-based virtual screening (SVS) heavily relies on scoring functions for hit identification.
  • Current scoring function development faces challenges in dataset creation and descriptor utility.

Purpose of the Study:

  • To present an alternative method for scoring function design in SVS.
  • To develop a scoring function that integrates crystallographic data with SVS calculation outputs.
  • To address limitations of existing scoring functions by utilizing 'noise' compounds.

Main Methods:

  • A genetic algorithm (GA) was employed to optimize scoring functions.
  • Binding property data was derived from multiple SVS calculations on Protein Data Bank (PDB) complexes.

Related Experiment Videos

  • Ligands with known binding modes and 'noise' compounds were used in calculations.

    • Main Results:

    • The developed scoring function does not require experimental assay data.
    • The approach can potentially identify sub-optimal docking interactions inherent in SVS.
    • Initial comparisons with existing DOCK scoring functions were performed.

    Conclusions:

    • The proposed method offers a novel strategy for scoring function development in SVS.
    • Integrating direct SVS data with structural information can enhance scoring function performance.
    • Further research is needed to explore dataset creation and descriptor utility limitations.