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
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?