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

Knowledge-based interaction fingerprint scoring: a simple method for improving the effectiveness of fast scoring

Chidochangu P Mpamhanga1, Beining Chen, Iain M McLay

  • 1Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom.

Journal of Chemical Information and Modeling
|March 28, 2006
PubMed
Summary

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

Synthesis of Phenyl 2-Acetamidoselenogalactoside Mimetics and Interaction with Amyloid β<sub>1-42</sub>.

Pharmaceuticals (Basel, Switzerland)·2026
Same author

Development and application of an ion sensitive probe for helicon plasma diagnostics.

The Review of scientific instruments·2025
Same author

Synthesis, crystal structure and Hirshfeld surface analysis of Fmoc-β-amino butyric acid and Fmoc carbamate.

Acta crystallographica. Section E, Crystallographic communications·2025
Same author

Searching chemical databases in the pre-history of cheminformatics.

Journal of cheminformatics·2024
Same author

Hierarchically spherical assembly of carbon nanorods derived from metal-organic framework as solid-phase microextraction coating for nitrated polycyclic aromatic hydrocarbon analysis.

Journal of chromatography. A·2024
Same author

Chaperone BiP controls ER stress sensor Ire1 through interactions with its oligomers.

Life science alliance·2024

A novel computational method enhances drug discovery by encoding 3D binding modes into bit strings. This knowledge-based scoring significantly improves the identification of potential drug candidates compared to traditional methods.

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Traditional scoring functions in molecular docking can be limited in accurately ranking binding modes.
  • Effective postprocessing of docking outputs is crucial for identifying high-quality drug candidates.

Purpose of the Study:

  • To develop and validate a new knowledge-based scoring method for postprocessing molecular docking outputs.
  • To assess the performance of the new method in recovering known binding modes and identifying diverse sets of molecules.

Main Methods:

  • Encoding 3D binding modes as ligand-protein interaction bit strings, analogous to structural interaction fingerprints.
  • Utilizing knowledge-based scores derived from bit string similarity to a reference binding mode.
  • Applying the method to a GOLD docking study of estrogen receptor antagonists.

Related Experiment Videos

Main Results:

  • The new knowledge-based scoring method demonstrated superior recovery rates, achieving up to 2-fold enrichment compared to the GOLD fitness score.
  • Top-ranked molecules exhibited structural diversity with low molecular weights and complexity.
  • Principal component analysis and clustering of fingerprints effectively separated active from inactive binding modes.

Conclusions:

  • The developed bit string encoding and knowledge-based scoring method offers a powerful approach for postprocessing docking results.
  • This method enhances the identification of relevant binding modes and facilitates the discovery of structurally diverse drug candidates.
  • The approach aids in visualizing and separating diverse binding modes, improving drug discovery efficiency.