Article ID: 824 - Last Modified: September 30, 2011
Why do I need to dock my library created with the Combinatorial Screening workflow in the final step again, although there was already a docking step during the library creation?
In the Combinatorial Screening workflow, the virtual space can contain millions of structures. CombiGlide samples these structures but does not enumerate this entire library. It uses a selection algorithm based on docking cores with all possible single substitutions at each of the positions to eliminate reagents, then selects fully substituted structures based on the single-substitution results by a selection algorithm that chooses the likely good binders. This final docking stage only gives a sample of the fully substituted structures, it does not dock all possible combinations, even after eliminating reagents. In the final step, you exclude reagents from certain positions and subject this library to certain criteria like GlideScore or property filters, and end up with a significantly smaller library. However, there is no guarantee that all the members of this library have been docked, though some of them must have been docked. This is why your selected small library is enumerated and docked in the final step of this workflow: to ensure that you have docking results for all compounds in this small library.
Keywords: Docking, Combinatorial Screening, CombiGlide, Maestro
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