Member Site Forums PyRosetta PyRosetta – General Peptide design Reply To: Peptide design


    The short answer, it’s impossible.

    It’s very hard to do efficiently; there is some multistate design code in 3.2 (and a HUGE AWESOME new mode coming in 3.3 that solves the problem very efficiently and generically). I don’t know if any of this was wrapped for Pyrosetta, I would guess not.

    The usual alternative is to re-rank results by binding energy after searching based on total energy. Results poor in total energy but great in binding energy are suspicious, so this is not a poor solution.

    If you are redesigning a small peptide, your search space may be small enough to brute-force search it? How big is the sequence space you want to examine?