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Comparison of shape-matching and docking as virtual screening tools.

Paul C D Hawkins¹, A Geoffrey Skillman, Anthony Nicholls

¹OpenEye Scientific Software, Santa Fe, New Mexico 87507, USA. phawkins@eyesopen.com

Journal of Medicinal Chemistry

|January 5, 2007

Summary

Shape-based virtual screening methods are more consistent and effective than traditional ligand docking for identifying drug candidates. This ligand-centric approach offers a superior alternative to protein-centric docking strategies.

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

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
Drug discovery
Bioinformatics

Background:

Ligand docking is a common virtual screening technique.
Docking effectiveness varies significantly due to confounding factors.
Shape-based, ligand-centric methods show promise for virtual screening.

Purpose of the Study:

Compare the effectiveness of ligand docking versus shape-based virtual screening.
Evaluate the consistency and superiority of different virtual screening approaches.
Analyze performance using recent docking benchmark datasets.

Main Methods:

Direct comparison of docking with the shape-based tool ROCS.
Utilized datasets from recent publications comparing docking tools.
Evaluated virtual screening effectiveness against various protein targets.

Main Results:

Shape-based, ligand-centric approaches demonstrate greater consistency than docking.
The ligand-centric method often outperforms traditional protein-centric docking.
Docking performance is highly variable and influenced by multiple factors.

Conclusions:

Shape-based virtual screening offers a more reliable and effective strategy.
Ligand-centric methods provide a superior alternative to protein-centric docking.
This finding has implications for optimizing virtual screening in drug discovery.