I have modelled wild type and mutant structures, generated by comparative modelling. There is no significant change in secondary structures in mutants with respect to wild type. Though I am expecting changes in thermodynamic level. I am also aware of some softwares that can serve the purpose. But really want to know what researchers are using most. Please suggest.
Thanks in advance.
One of the most commonly used tools to predict changes in free energy in order to determine impact on folding/unfolding(I hope that is what you want to do) is FoldX. Although there are plently of other servers which do the same like SDM etc. my own experience suggests that FoldX works pretty well. On the other hand if you can perform a long running MD simulation(depends on how big your protein is) you can do it yourself without any server.
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