Hi all,
I am trying to implement the method outlined in "Incorporation of Noncanonical Amino Acids into Rosetta and use in Computational Protein- Peptide Interface Design" doi:10.1371/journal.pone.0032637.
I just wondered if I should start right from the beginning, or whether there is somewhere I can download the parameter files, rotamer libraries and unfolded state reference energies for NCAAs so that I can move directly to doing the design protocol.
Any advice would be most appreciated.
wsgosal
Post Situation:
Hi Walraj, I think we met at RosettaCon. Thanks for your interest in the NCAA paper. The ResidueType parameter files are distributed with Rosetta but are not enabled/turned-on by default. The rotamer libraries are not however are not distributed with Rosetta. You can download them at the link below.
http://carl.bio.nyu.edu/~renfrew/ncaa/ncaa_rotamer_libraries.tar.gz
Here is a quick reference for the three letter codes for the NCAAs
http://fry2.bio.nyu.edu/~kdrew/rosetta/ncaa_codes
I suspect that you will also find the protocol capture associated with this paper rather useful. You can find it in the demos directory of your copy of Rosetta.
The carl.bio.nyu.edu link appears to be broken now - are these still available somewhere?
Try the following DropBox links from Doug Renfrew:
https://www.dropbox.com/s/a3g0caisrlan09j/ncaa_rotamer_libraries.tar.gz?dl=0
https://www.dropbox.com/s/fqd7ywy1wzk6ujm/beta_amino_acid.tar.gz?dl=0
https://www.dropbox.com/s/98l2lpshncdlqur/peptoid_rotlibs_kmc.tar.gz?dl=0
Thanks for these!
By any chance do you have a key for the three letter codes used for the NCAAs?
The previously posted link seems to have also died.
Thanks!
http://fry2.bio.nyu.edu/~kdrew/rosetta/ncaa_codes
is not accessible.
Is there a updated website?
I have no idea about that link but I was curious too about what NCAA were available in the database folder, so I made a table: https://github.com/matteoferla/Display-of-preset-Rosetta-NCAAs
Hi Doug,
Yes we did and thanks so much for this - really appreciate the help. Will let you know how I get on.
Best,
W.
Hi All,
How do you generate parameters for a stapled helix peptide? The residues that are "stapled" are alanines at position 1 and 5, inclusive. The "staple" is a 8-carbon linker.
Thanks!