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Related Experiment Video

Updated: Jul 17, 2026

Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology
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Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology

Published on: March 31, 2022

Scoring functions and enrichment: a case study on Hsp90.

Chrysi Konstantinou-Kirtay1, John B O Mitchell, James A Lumley

  • 1Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK. ck302@cam.ac.uk <ck302@cam.ac.uk>

BMC Bioinformatics
|January 30, 2007
PubMed
Summary

Virtual screening effectively identifies drug candidates using scoring functions. Optimizing docking protocols with specific tethers and normalization significantly improves enrichment of active compounds against Hsp90.

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Exploring Biomolecular Interaction Between the Molecular Chaperone Hsp90 and Its Client Protein Kinase Cdc37 using Field-Effect Biosensing Technology
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Malachite Green Assay for the Discovery of Heat-Shock Protein 90 Inhibitors
07:57

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Published on: January 20, 2023

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Molecular modeling

Background:

  • High-throughput screening (HTS) and in silico virtual screening accelerate early-stage drug development.
  • Accurate scoring functions are crucial for identifying potential drug candidates efficiently.
  • Heat shock protein 90 (Hsp90) is a key target in drug discovery.

Purpose of the Study:

  • To evaluate the discriminatory power of common scoring functions (GOLD, ChemScore, DOCK, PMF, BLEEP, Consensus) in virtual screening.
  • To investigate the impact of different ranking methodologies and docking strategies on screening enrichment.
  • To assess the effectiveness of normalization and specific tethers in improving virtual screening performance.

Main Methods:

  • Comparison of GOLDrank and BestScorerank methodologies.
  • Application of scoring functions to a library of ~3,600 diverse decoy compounds against Hsp90.
  • Evaluation of the Thr184 hydrogen bond tether for guiding docking.
  • Implementation of normalization for molecular weight bias.

Main Results:

  • Most scoring functions showed similar enrichment, with PMF being the poorest performer.
  • GOLD marginally outperformed other individual functions; Consensus performed comparably to the best single function.
  • The combination of the Thr184 tether, BestScorerank protocol, and molecular weight normalization yielded the best results.
  • DOCK and Consensus recovered 90% and 89% of active compounds in the top 10% of the ranked list, respectively.

Conclusions:

  • Virtual screening is a valid method for identifying new leads from diverse ligand pools.
  • The study provides insights into optimizing docking and scoring protocols for improved enrichment of active compounds.
  • Tailored protocols can enhance the efficiency of virtual screening in drug discovery.