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How to do an evaluation: pitfalls and traps.

Paul C D Hawkins1, Gregory L Warren, A Geoffrey Skillman

  • 1OpenEye Scientific Software, 9, Bisbee Court, Suite D, Santa Fe, NM 87508, USA. phawkins@eyesopen.com

Journal of Computer-Aided Molecular Design
|January 25, 2008
PubMed
Summary
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Evaluating computational tools for drug discovery requires careful consideration of dataset bias and performance metrics. Many studies overlook critical factors affecting the reliability of docking and virtual screening results.

Area of Science:

  • Computational chemistry
  • cheminformatics
  • drug discovery

Background:

  • Numerous studies evaluate computational tools for molecular docking and virtual screening.
  • These evaluations commonly focus on pose prediction and screening performance.
  • Existing literature often overlooks critical factors influencing the reliability of these assessments.

Purpose of the Study:

  • To highlight critical factors affecting the reliability of computational tool evaluations.
  • To address the common oversight of dataset bias, metric selection, and structural errors in performance assessments.

Main Methods:

  • Review of existing literature on computational tool performance evaluation.
  • Identification of common methodologies and their inherent limitations.

Related Experiment Videos

  • Analysis of factors impacting the accuracy of virtual screening and pose prediction.

    • Main Results:

    • Evaluations of computational tools often suffer from biased datasets.
    • The choice of performance metrics significantly impacts reported results.
    • Errors in experimental structures (e.g., crystal structures) compromise tool assessment reliability.

    Conclusions:

    • The reliability of computational tool comparisons in drug discovery is questionable due to overlooked factors.
    • Future evaluations must address dataset bias, appropriate metric selection, and data quality.
    • Standardized, rigorous evaluation protocols are needed for accurate computational tool assessment.