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null mutation with ddg_monomer

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null mutation with ddg_monomer

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,

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Fri, 2012-05-11 07:16

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?

Fri, 2012-05-11 07:28

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.

Fri, 2012-05-11 08:28

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.

Fri, 2012-05-11 08:33

Ok, thank you for helping.

Fri, 2012-05-11 08:41