If you don’t know the sequence, you can start with an arbitrary sequence,as long as the length is the right. However, you do need to think about the secondary structure propensity, for instance, it’s not good to put all ALA in beta strand.
> Hi all,
> I’m playing around with designing a new protein de novo (a la Top7) for the first time, and I am wondering what sequence I should put in the fasta file for both building the fragment library and during the generation of tertiary structure by fragment assembly. Obviously, I don’t know what the sequence of the final protein should be, but both fragment selection and assembly seem to require a valid fasta file.
> Any ideas for a beginning designer on what the best approach is here? Thanks in advance!