Protein Structure Prediction using PyRosetta, suggestions wanted :)

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    • #1279
      Anonymous

        Hello!

        Im trying to write a de novo folding script with pyrosetta (PyRosetta
        v2.011 for windows).

        I’m trying to follow the approach described in this paper:

        Alena Shmygelska and Michael Levitt; Generalized ensemble methods for
        de novo structure prediction, PNAS February 3, 2009 vol. 106 no. 5
        1415-1420

        that in turn refers to

        Rohl, et all; Protein Structure Prediction using Rosetta, methods in
        enzymology vol 383, 2004.

        Right now I’m using only low resolution centroid score functions
        because I’m not interested in the all-atom refinement stage in my project
        (that is something similar to the first paper I cited, i.e. I am
        applying replica exchange method to the abinitio protocol)

        here I list the main steps of my folding script:

        starting from the extended chain configuration

        1-I apply 2000 random 9-residue fragment insertions, accepting them
        according to the metropolis criterion and using score0

        2- 2000 random 9-residue fragment insertions accepting them according
        to the metropolis criterion and using score1

        3- 20.000 random 9-residue fragment insertions, accepting them
        according to the metropolis criterion. Every 2000 insertions i switch
        between score2 and score 5

        4- 2000 random 9-residue fragment insertions, accepting them according
        to the metropolis criteria and using score3

        5- 8000 random 3-residue fragment insertions, accepting them according
        to the metropolis criteria and using score3

        I am not interested in implementing the latest abinitio protocol. I
        would rather try to copy exactly the classic abinitio protocol
        performed in the first paper.

        Is the protocol similar to the default classic abinitio?
        Is there something I forgot or that you think I should add?
        I will start testing it soon and it would be great if anyone has any
        suggestions

      • #7120
        Anonymous

          oppopomoz, this sounds about right. Though, there may have been changes in the score function between then and now. Why not use the current executable?

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