Noncanonical amino acids

[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

[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.

[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.

[Anonymous]

The carl.bio.nyu.edu link appears to be broken now – are these still available somewhere?

[Anonymous]

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

[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!

[Author]

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