Help with flexible backbone design

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    • #308

        Hello all,

        I am trying to hone my de novo design skills by reproducing de novo
        designs of Top7 as described by Kuhlman, et al. (2003). So far, I can
        generate sequence-independent starting models that I am confident are
        good, but I am clearly not doing well on the flexible backbone design
        step. After flexible backbone design, my best per residue LJ
        attractive energies are around -3.1 per residue, whereas the same
        value reported in Table S1 from Kuhlman, et al. (2003) is about -4.1
        per residue (-385 / 93 resis). I also frequently get structures that
        ‘blow up’; they are no longer compact globules, but very extended

        My resfile is set up to allow only polar amino acids on the
        solvent-exposed side of the beta sheet, and everything but cysteine
        everywhere else, as described for Top7.

        I have tried flexible backbone design without a weights file (default
        weights), or giving Rosetta the weights listed in Table S6 from
        Kuhlman, et al. (2003) both with and without the unique reference
        energies for each amino acid in a -weightfile. I find that when I use
        the reference energies listed in that table I get sequences extremely
        heavy in E, D, and K, which means that the reference energy term is
        dominating everything else.

        Here is the command that I am running:

        rosetta.gcc XX ABCD A
        -extrachi_cutoff 1
        -resfile top7.resfile
        -s ABCD.pdb
        -paths paths.txt

        My results clearly suggest that I am not doing something right, but I
        can’t figure out what it might be. Any help would be greatly
        appreciated. Thanks in advance!


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