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Yes, it is correct if the conserved domain is independent folding unit (if the conserved domain can be found in different domain context in unrelated proteins it is very likely to be the case). However, if it closely interacts with other domains with big hydrophobic patch you might run into problems (rosetta might try to push the should-be-surface hydrophobic residues to the core).
In your case I think the problems are due to the protein length and many many more decoys as well as more sophisticated rosetta approaches might be needed (with no guarantee of success).
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> is it correct if i just using a domain which is conserved domain according to the domain prediction server. i just remove N and C terminal to make my protein smaller from 295 aa to 176 aa.
> or any other suggestion
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> thanks
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> Hasni