Hi Rosetta users,
Has anybody happen to know if Rosetta's ddg_monomer can deal with a null mutation (deletion)?
I've read that ddg_monomer cannot handle mutations to cysteine. Please, could someone tell me why? Also, is there a overcome to analyse mutations to cysteine?
All the Best,
I'm 99% sure it can't handle indels. Indels require significant backbone rearrangements - probably more than ddg can do. You can model indels with loop modeling instead.
I do not know that ddg_monomer will refuse to test cysteine, but if it will, it's a refusal to deal with disulfides. It may also be that there are too few mutations to cysteine available in the literature for benchmarking. Did you try it?
Actually, such mutation lays in a helix. Sounds interesting to treat few adjacent residues as loop. But, how should I have to treat the remaining residues around deletion?
I haven't tried it, yet. However, disulfide formation would probably be my case. There is a CYS just before the mutation.
You'd have to remake a whole homology model of your deletion to determine how and if the helix rotates to account for the sequence shift. This is not a trivial thing to do and way beyond what ddg_monomer will do.
Ok, thank you for helping.