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Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial

Authors

  • Graham R. Smith,

    1. Department of Biological Sciences, Biochemistry Building, Imperial College of Science, Technology and Medicine, London, United Kingdom
    2. Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, London, United Kingdom
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  • Michael J.E. Sternberg

    Corresponding author
    1. Department of Biological Sciences, Biochemistry Building, Imperial College of Science, Technology and Medicine, London, United Kingdom
    • Department of Biological Sciences, Biochemistry Building, Imperial College of Science, Technology and Medicine, London SW7 2AZ, United Kingdom
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Abstract

The 3D-Dock suite of programs has been used to make predictions for the seven targets in rounds 1 and 2 of the CAPRI method evaluation exercise. Some correct contacts were obtained in at least one prediction for four of seven targets. Target 06 was predicted very well, with an RMSD of the ligand after superimposition of the receptor of only 0.77 Å. We investigate the performance of the various stages of the method, with the aim of finding where improvements need to be made, and in particular whether the manual interventions that were made were essential, and whether results of the level of accuracy obtained for target 06 may be expected with confidence. Proteins 2003;52:74–79. © 2003 Wiley-Liss, Inc.

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