Journal of Computer-Aided Molecular Design

, Volume 26, Issue 8, pp 897–906 | Cite as

FRED and HYBRID docking performance on standardized datasets

Article

Abstract

The docking performance of the FRED and HYBRID programs are evaluated on two standardized datasets from the Docking and Scoring Symposium of the ACS Spring 2011 national meeting. The evaluation includes cognate docking and virtual screening performance. FRED docks 70 % of the structures to within 2 Å in the cognate docking test. In the virtual screening test, FRED is found to have a mean AUC of 0.75. The HYBRID program uses a modified version of FRED’s algorithm that uses both ligand- and structure-based information to dock molecules, which increases its mean AUC to 0.78. HYBRID can also implicitly account for protein flexibility by making use of multiple crystal structures. Using multiple crystal structures improves HYBRID’s performance (mean AUC 0.80) with a negligible increase in docking time (~15 %).

Keywords

Docking Virtual screening FRED HYBRID DUD Protein flexibility 

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Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.OpenEye Scientific SoftwareSanta FeUSA
  2. 2.OpenEye Scientific SoftwareCambridgeUSA

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