Member Site › Forums › PyRosetta › PyRosetta – Scripts › Protein Structure Prediction using PyRosetta, suggestions wanted :)
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May 15, 2012 at 4:40 pm #1279Anonymous
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
1415-1420that 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 score02- 2000 random 9-residue fragment insertions accepting them according
to the metropolis criterion and using score13- 20.000 random 9-residue fragment insertions, accepting them
according to the metropolis criterion. Every 2000 insertions i switch
between score2 and score 54- 2000 random 9-residue fragment insertions, accepting them according
to the metropolis criteria and using score35- 8000 random 3-residue fragment insertions, accepting them according
to the metropolis criteria and using score3I 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 -
May 16, 2012 at 2:15 pm #7120Anonymous
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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