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Updated: May 8, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Methods for docking small molecules to macromolecules: a user's perspective. 2. Applications.

Valérie Campagna-Slater, Eric Therrien, Nathanael Weill

  • 1Department of Chemistry, McGill University, 801 Sherbrooke St W, Montreal, Qc, Canada H3A 0B8 and Molecular Forecaster Inc., 969 Marc-Aurele Fortin, Laval, Qc, Canada, H7L 6H9. nicolas.moitessier@mcgill.ca.

Current Pharmaceutical Design
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PubMed
Summary
This summary is machine-generated.

Molecular docking methods are widely used for hit identification and drug discovery. This review explores their diverse applications beyond initial screening, including de novo design and predicting drug interactions.

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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Area of Science:

  • Computational chemistry and drug discovery

Background:

  • Numerous research articles detail novel molecular docking and scoring methodologies.
  • Publications frequently report successful applications in identifying novel hit molecules.

Purpose of the Study:

  • To review the broader applications of molecular docking methods beyond hit identification.
  • To highlight the utility of docking in diverse areas of drug discovery and development.

Main Methods:

  • Literature review of studies employing molecular docking techniques.
  • Categorization of applications based on their role in the drug discovery pipeline.

Main Results:

  • Documented applications of docking extend to de novo design and fragment-based drug discovery.
  • Docking methods are also applied to lead optimization, metabolism prediction, and off-target binding analysis.
  • Further applications include assessing selectivity, protein structure prediction, and drug-drug interactions.

Conclusions:

  • Molecular docking is a versatile computational tool with applications spanning the entire drug discovery process.
  • Expanding the documented use of docking can accelerate the development of new therapeutics.