Frequently asked questions

How should the starting structure be selected for running the cryptic pocket detection floes?

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