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Workflow and Tools for Crystallographic Fragment Screening at the Helmholtz-Zentrum Berlin
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Theoretical and practical considerations in virtual screening: a beaten field?

Maria Kontoyianni1, Prakash Madhav, Eric Suchanek

  • 1Procter & Gamble Pharmaceuticals Inc., 8700 Mason Montgomery Road, Mason, OH 45040, USA. mkontoyi@yahoo.com

Current Medicinal Chemistry
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PubMed
Summary

This review covers virtual screening techniques, including docking and ligand-based methods. It details classification of docking programs and scoring functions, addressing protein flexibility and offering best practices for enhanced hit rates.

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Area of Science:

  • Computational chemistry
  • Drug discovery
  • Bioinformatics

Background:

  • Virtual screening (VS) is crucial for identifying drug candidates.
  • Docking and scoring are established VS techniques.
  • Ligand-based VS is increasingly important.

Purpose of the Study:

  • To review various virtual screening methodologies.
  • To classify and describe current docking programs and scoring functions.
  • To discuss challenges and best practices in VS.

Main Methods:

  • Classification of docking programs based on underlying theories.
  • Categorization and discussion of scoring functions and their weighting schemes.
  • Analysis of protein flexibility and selection strategies for docking/scoring.

Main Results:

  • Docking programs are categorized into four types.
  • Scoring functions are presented in three categories with binding term discussions.
  • A case study demonstrates iterative pharmacophore and docking for improved hit rates.

Conclusions:

  • Understanding docking and scoring function nuances is key for target-specific selection.
  • Addressing protein flexibility is critical for accurate VS.
  • Iterative approaches combining pharmacophore modeling and docking enhance virtual screening success.