Reply To: ulfated tyrosine in Rosetta

[Anonymous]

Hi.

I faced a similar issue because I needed to model statherin
and to introduce phosphoserines(SEP) in Rosetta forcefield
http://oasys2.confex.com/acs/232nm/techprogram/P986054.HTM.external link

As you see Rosetta has a mode -phospho_ser,
which if you added in the options,
you’ll be able to model proteins with SEP(eg 1F8A)
from Protein Data Bank.
In order to do this someone needs to add other amino-acid properties
such as rotamer statistics in Rosetta_database
and please find some brief comments in add_pser.cc.

Right now Rosetta doesn’t support other modified residues
and there is not a simple recipe which source files to modify,
in order to model them.
In the future releases Rosetta will be extended
to a more general recipe for such modifed amino-acids.

Best,
Kosta

> Hi,
>
> I have started to use RosettaDock for docking a protein (coordinates from
> crystal structure) to a peptide (coordinates from NMR). The peptide contains
> 2 sulfated tyrosine residues (named TYS). Rosetta is not being able to
> recognize these residues and is giving the error message “unrecognized
> residue: TYS”.
>
> How can I address this problem?
>
> Thanks in advance.
>
> Sincerely,
> Priyamvada
>
>