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Better than random? The chemotype enrichment problem.

Mark D Mackey¹, James L Melville

¹Cresset BioMolecular Discovery Ltd., BioPark Hertfordshire, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom. mark@cresset-bmd.com

Journal of Chemical Information and Modeling

|April 29, 2009

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Chemotype enrichment is vital for virtual screening. This study reveals that the "first found" method for quantifying chemotype retrieval has significant drawbacks when used with quantitative metrics, unlike "cluster averaging".

Area of Science:

Computational chemistry
Cheminformatics
Drug discovery

Background:

Chemotype enrichment is a key metric for evaluating virtual screening performance.
Quantifying chemotype retrieval in virtual screening remains underexplored.
Existing qualitative analyses often use methods with potential quantitative drawbacks.

Purpose of the Study:

To examine and compare two protocols for analyzing chemotype retrieval: "cluster averaging" and "first found".
To identify the drawbacks of the "first found" protocol when applied to quantitative metrics in virtual screening.

Main Methods:

Analysis of two distinct chemotype retrieval protocols: "cluster averaging" and "first found".
Evaluation of how each active contributes to scoring metrics based on chemotype similarity.

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Comparison of the impact of these protocols on quantitative performance metrics.

Main Results:

The "cluster averaging" method weights actives based on the number of similar chemotypes.
The "first found" method only considers the initial identification of a chemotype.
The "first found" analysis, though common qualitatively, presents significant limitations for quantitative virtual screening metrics.

Conclusions:

The choice of protocol for analyzing chemotype retrieval significantly impacts virtual screening performance assessment.
"Cluster averaging" offers a more robust approach for quantitative chemotype retrieval analysis.
The "first found" method should be used with caution in quantitative virtual screening evaluations due to inherent drawbacks.