I am attempting to predict the structure of a metalloenzyme after 5 mutations using the relax function. My current protocol consists of adding the following:
- Adding a mutation to the protein in pymol
- Relaxing the protein and picking the lowest energy structure
- Adding another mutation to the lowest energy structure and repeating until all mutations have been added.
Would this be the best protocol to perform this action or would it be better to just add all the mutations at once and then relax the protein? Also is there a better Rosetta program for doing this or for adding mutations? I have been getting good results but I was curious if there was a flaw in my protocol.