Member Site › Forums › Rosetta 3 › Rosetta 3 – Applications › Noncanonical amino acids
- This topic has 5 replies, 5 voices, and was last updated 4 years, 2 months ago by
Anonymous.
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March 18, 2014 at 12:29 pm #1853
Anonymous
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
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March 21, 2014 at 3:50 pm #9914
Anonymous
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.
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March 25, 2014 at 9:32 am #9919
Anonymous
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.
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April 10, 2016 at 7:58 pm #11507
Anonymous
The carl.bio.nyu.edu link appears to be broken now – are these still available somewhere?
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April 29, 2016 at 2:49 pm #11549
Anonymous
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June 30, 2020 at 3:43 pm #15362
Anonymous
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!
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