I want to design the sequences of an enzyme. I am not sure which method should I use. I am thinking of 2 methods:
1. Use fixbb and fix the enzyme site of the protein. just design the other part of the protein
2. Use Enzyme Design of rosetta 3.3. But this program seems only design the active sites.
If you are trying to alter enzyme activity, you need to use the enzyme design suite. If you are altering the sequence far from the active side, fixbb is better. If you want to change the sequence at or near the active site, you could use either; fixbb will be hugely faster and easier to use but enzyme design will attempt to maintain enzymatic activity (which fixbb won’t).