A total of 20 research groups submitted results for the 2011 CSAR benchmark exercise where the goal was to compare different improvements for docking and relative ranking of congeneric series of compounds. The exercise was built around blinded, high-quality experimental data from four protein targets: urokinase, Chk1, ERK2, and LpxC. Here, we outline our efforts to evaluate this generous contribution from the community. When developing computational methods, proper evaluation of the results is just as important as the high quality experimental data used in the training set. RMSD is the standard for evaluating poses, but it can be misleading. Native-contact metrics can capture the complex interactions and, used in combination with the RMSD, provides a more robust evaluation of the predicted poses. Other assessment metrics will also be presented. Lastly, we have evaluated the ability of scoring functions to properly identify the inactives in the series and their ability to rank-order the active compounds.

Community structure-activity resource (CSAR) benchmark exercise 2011: Docking and relative ranking of a blinded congeneric series of compounds

244th National Meeting (2012)

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