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 of filter functions for protein-ligand docking.

M Stahl1, H J Böhm

  • 1Hoffmann-La Roche, Ltd., Pharmaceuticals Division, Basel, Switzerland. martin.stahl@roche.com

Journal of Molecular Graphics & Modelling
|August 6, 1999
PubMed
Summary

This study introduces a new filtering method to improve protein-ligand docking accuracy. The approach uses four key properties to efficiently remove incorrect structures and rescore remaining predictions.

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

First Measurement of Time-Dependent CP Violation in the Flavor-Changing Neutral-Current Decay B^{0}→K_{S}^{0}μ^{+}μ^{-}.

Physical review letters·2026
Same author

Measurement of the Top-Quark Production Cross Section and Charge Asymmetry at LHCb.

Physical review letters·2026
Same author

Searches for B^{0}→K^{+}π^{-}τ^{+}τ^{-} and B_{s}^{0}→K^{+}K^{-}τ^{+}τ^{-} Decays.

Physical review letters·2026
Same author

First Evidence of the B_{s}^{0}→K^{-}π^{+}γ Decay.

Physical review letters·2026
Same author

Patients' Symptoms and Support Needs at Start of Specialized Palliative Care Therapy in an Inpatient Oncology Setting. A Retrospective Data Analysis.

The American journal of hospice & palliative care·2026
Same author

Precision Measurement of CP Violation and Branching Fractions in B^{±}→K_{S}^{0}h^{±} (h=π, K) Decays and Search for the Rare Decay B_{c}^{±}→K_{S}^{0}K^{±}.

Physical review letters·2026

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Protein-ligand docking methods predict binding conformations.
  • Current scoring functions often fail to rank accurate predictions highest.

Purpose of the Study:

  • To develop a computationally efficient postprocessing scheme for docking results.
  • To improve the accuracy of protein-ligand complex structure predictions.

Main Methods:

  • Calculated four properties for each docked conformation: buried ligand volume fraction, lipophilic cavity size, nonpolar ligand solvent-accessible surface (SAS), and non-hydrogen-bonded polar atom contacts.
  • Applied these properties as filter functions to remove unfavorable structures.
  • Rescored the remaining filtered conformations.

Related Experiment Videos

Main Results:

  • The developed protocol significantly enhances the accuracy of structure predictions for protein-ligand complexes.
  • Effectively filters out a majority of incorrect docked conformations.
  • Demonstrated improvement on a test set of 32 protein-ligand complexes.

Conclusions:

  • The proposed filtering scheme offers a reliable and efficient method for improving protein-ligand docking accuracy.
  • This approach addresses limitations of current scoring functions in structure-based drug design.
  • Enables more accurate identification of correct binding poses.