I would like to compare stability of the wild-type and mutated proteins(multi-metric enzyme) using cartesian_ddg. But I am confused about which one is suitable structure input. And I have two ideas now:
- Relax the whole enzyme, calculate each chains' ddg, and finally average the numbers.
- Split the enzyme complex into subunit monomers, calculate each monomers' ddg, and finally average the numbers.
Which one is the most suitable choice?
About 1, is the relax app works well on complex structure? About 2, I think the movement in former subunit interface will be more aggressive, is it still right?
Thanks in advance for any responses on this question.