how to get around no sequence for de novo design?

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    • October 6, 2008 at 10:01 pm #304
      norn
      Participant

        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!

        -Neil

      • October 7, 2008 at 2:24 pm #4018
        Ora Furman
        Participant

          Hi,

          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!
          >
          > -Neil

        • October 7, 2008 at 3:55 pm #4019
          norn
          Participant

            Thanks for the response, huxz.

            I looked through some of the scoring function code yesterday, and I think I might maybe kinda sorta possibly understand a little better how to do this now… It looks like when designing proteins de novo you want to only go through the first few stages of scoring (bump check first, then ss & light strand pairing, etc.), but not the later stages where centroids are added in for the side chains and the chain is collapsed? That way you get backbone models “generated without regard to side-chain packing” (Kuhlman et al., describing Top7), right? I was confused before because I was worried that if I put in poly-Ala or something as my sequence that the starting models would be packed too tightly to allow mutation to larger side chains later. But if you cut out the later scoring stages that take side chains into account (the sequence-specific part of the scoring function), then this isn’t a problem.

            Is that correct?

            Thanks again!

            Neil

          • October 9, 2008 at 2:43 pm #4020
            Ora Furman
            Participant

              That is right.
              > 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!
              >
              > -Neil

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