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Related Experiment Videos

Comparative study of several algorithms for flexible ligand docking.

Badry D Bursulaya1, Maxim Totrov, Ruben Abagyan

  • 1Department of Molecular Biology (TPC6), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Journal of Computer-Aided Molecular Design
|April 10, 2004
PubMed
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This study compared molecular docking software, finding ICM 2.8 most accurate for ligand docking. FlexX was fastest, while ICM excelled in virtual screening accuracy.

Area of Science:

  • Computational chemistry
  • Drug discovery
  • Structural biology

Background:

  • Flexible molecular docking is crucial for identifying potential drug candidates.
  • Several software programs exist, but their comparative performance in accuracy and speed is not well-established.

Purpose of the Study:

  • To comparatively assess the accuracy and speed of flexible molecular docking programs.
  • To evaluate the performance of DOCK 4.0, FlexX 1.8, AutoDock 3.0, GOLD 1.2, and ICM 2.8.
  • To determine the most effective software for virtual database screening.

Main Methods:

  • Comparative assessment of five molecular docking programs: DOCK, FlexX, AutoDock, GOLD, and ICM.
  • Two studies were conducted: docking 37 protein-ligand complexes and screening 10,037 compounds against 11 proteins.

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  • Accuracy was evaluated by rank-one solutions, and speed was measured for docking and screening.

    • Main Results:

    • ICM 2.8 demonstrated the highest docking accuracy (0.93), significantly outperforming others.
    • FlexX was the fastest program, while AutoDock was the slowest.
    • In virtual screening, ICM identified original ligands within the top 1% in 17 cases, superior to DOCK (7) and FlexX (8).

    Conclusions:

    • ICM 2.8 is the most accurate software for flexible ligand docking and virtual screening.
    • FlexX offers the best speed-performance ratio among the tested programs.
    • The findings provide valuable guidance for selecting appropriate molecular docking tools in drug discovery pipelines.