Frequently Asked Questions

How should the starting structure be selected for running the Target X floes?

Selection of the starting structure for running the floe_AutomatedTargetXwithProbeOccupancyAnalysis Floe depends on the objective of running the floe. If the user is running the floe for validation purposes, the starting structure should be an apo structure of the protein of interest. If the user is running the floe_AutomatedTargetXwithProbeOccupancyAnalysis Floe on their target protein, they should choose the state of the protein that best depicts the target state. For example, for finding a pocket that targets its oligomeric state, the user must ensure that the starting structure is in the correct oligomeric state. Similarly, the correct substrate bound state should be chosen as the starting structure if the pocket needs to be identified in a specific substrate bound state. For example, finding pockets in KRas in its inactive state requires the presence of GDP at its nucleotide-binding site.