Comments on the article "On evaluating molecular-docking methods for pose prediction and enrichment factors"

The recent article "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors" (Chen H. et al. J. Chem. Inf. Model. 2006, 46, 401-415) contains a series of comments on a similar study we published in Proteins in 2004 (Perola et al. Proteins 2004, 56, 235-249). We believe that some of these comments are misleading, and we feel that an adequate response is in order.