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Number of max allowed mutations from WT sequence

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Number of max allowed mutations from WT sequence

Hi folks,

I wonder if there is a way to constrain the number of maximal allowed mutations from the input sequence when doing a regular backbone-fixed design or a backbone-flexible design. For example, I only want the designed sequences away from the wild-type sequence by 5 residues at most (i.e. including 5, 4, 3, 2, and 1 mutations). Many thanks!



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Fri, 2020-09-04 02:33

After asking around, there doesn't seem to be a way to tell the part of Rosetta doing design to limit itself to a certain number of mutations from the wild-type sequence. There's a facility that could possibly be made to work, and there sounds like interest (independent of your question) in adding that functionality in, but nothing that exists currently.

What you could do now, though, is to use the FavorNativeResidue mover to add an adjustable bias toward the native residues. By dialing that value up and down you can cause Rosetta to change the likelihood of putting in mutations. At the right level, you should be able to get around a certain number of mutations.

That's not going to be exact, though. There's always a possibility of gettting more or fewer mutations than you've attempted to "dial in". If you really do have a hard limit at 5 mutations, you can use the MutationsFilter to throw out those structures with too many mutations.

Sun, 2020-09-06 10:10

Hi all, just wanted to add my +1 for developing this functionality if anyone is on the fence about doing it. Trying to fine tune FavornativeResidue or FavorSequenceProfile takes a lot of time and is very touchy. I think this would be a popular option.



Fri, 2021-02-12 08:53