I have produced a number of circular permutations for a protein. There are
several structures available for the wild type protein. Is MODELLER
able to process circular permutations? If so, how would I encode this in
my alignment file? Thanks in advance for your help!
I haven't tried modelling permuted forms before, but intuitively you may be able to do just that by aligning relevant segments of your permuted sequence to a different template model of your wild type protein ( just like you would do in case you are modeling a query sequence on multiple reference structures).I would definitely try that first. You can check the manual section on building model from multiple templates. It should work in your case, but I may be wrong.
Hope this helps.
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