Article ID: 1043 - Last Modified: June 2, 2011
Why am I getting large positive Prime energies in my Induced Fit Docking run?
Large positive Prime energies can come about when the protein has missing atoms, and as a result there are unfavorable interactions in the structure predicted by Prime due to poor side chain location. You can tell whether this is the case when you import the PDB structure: residues with missing atoms are colored red by Maestro.
To fix this problem, you should run a Prime refinement of the side chains before starting Induced Fit Docking, from the Prime Refinement panel, and choose all the residues that are colored red for the prediction. When the results are returned, check them carefully before choosing structures for Induced Fit Docking.
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