Reply To: Re : installation of rosetta 3.0 on fedora core 6

[Anonymous]

I am sorry for making my question a little bit confusing .. Actually there is a paper “High resolution Design of a protein Loop” in which they have used Rosetta for designing a loop of 10 residues for some protein .. I want to follow the same approach like the one given in paper .. For ur convenience I am stating here what they did …

1) they searched the pdb for residues that superimpose the loop residues of their protein..
2)they grafted these fragments on the protein using Monte CArlo optimization and gradient based mnimization , finally loop closure on basis of low energy backbone torsion angles , Hbonds and absence of clashes with neighbouring backbone atoms
3) From these simulation they selected 36 low scoring backbone str.
4) Each of the starting str (from those 36 was used to seed 200 independent sequence design and backbone optimization.

I also want to follow the same suite … but here I don’t have any backbone str. of loop to search a sequence as I want to insert longer loops in my protein… For that I have got a library of fragments of varied length from Prof. George Rose Lab, JHU …
Can I use that lib. together with kinematic loop modeling for that as they have mentioned in the documentation that they modeled a 10 residue loop for an 80 amino acid protein … Pls help ..

Today I was going through Pro. Brian’s site and I found ur name in there and the paper that I have mentioned above was published by one of ur group member…