disulfid bonds

[Anonymous]

Dear developers,

I am running CS-Rosetta on a protein with a known disulfide pattern and a large proportion of flexible structure. The first models look promising in terms of the recognition of some secondary structure elements (there is a X-Ray structure for the protein), however the overall tertiary structure perdiction is rather poor, which is due to the large flexible links between the secondary structure elements I believe. If I was able to use the known disulfide pattern as restraints the prediction would probably improve significantly. In my current setup the cysteines could not form bonds at all because they are too far from each other. Is there some way to change this? I found there’s a disulfide filter mentioned on the hoempage but could not figure out how I can possibly change its setting.

Many thanks and kind regards

Baerbel Blaum

[Anonymous]

According to my understanding, Rosetta does not consider/design disulfide in simulations. So maybe you can try to add a flag “-fix_disulf” to see whether this will help with your design. Check the manual for details of using this flag.

And, what do you mean CS-Rosetta?

> Dear developers,
>
> I am running CS-Rosetta on a protein with a known disulfide pattern and a large proportion of flexible structure. The first models look promising in terms of the recognition of some secondary structure elements (there is a X-Ray structure for the protein), however the overall tertiary structure perdiction is rather poor, which is due to the large flexible links between the secondary structure elements I believe. If I was able to use the known disulfide pattern as restraints the prediction would probably improve significantly. In my current setup the cysteines could not form bonds at all because they are too far from each other. Is there some way to change this? I found there’s a disulfide filter mentioned on the hoempage but could not figure out how I can possibly change its setting.
>
> Many thanks and kind regards
>
> Baerbel Blaum

[Anonymous]

Hi there,

thanks. I found the flag but I have difficulties figuring out what the additional files needs to look like that specifie the cysteine pairs. Basically the documentation mentions two files that need to be added, one for the flag -fix_disulf and a resfile where the cysteines are placed using PIKAA. Additionally I need to turn on the disulfide filter I think. I don’t get the design of the resfile though because it is not clear to me how to use the PIKAA option for disulfides.

CS-Rosetta stands for chemical shift Rosetta. It uses NMR data in addition to sequence similarity to select the fragments that will be used by Rosetta. The step I am struggling with is a pure Rosetta issue I think, so it doesn’t matter that I am using it as part of CS-Rosetta.

Baerbel

> According to my understanding, Rosetta does not consider/design disulfide in simulations. So maybe you can try to add a flag “-fix_disulf” to see whether this will help with your design. Check the manual for details of using this flag.
>
> And, what do you mean CS-Rosetta?
>
> > Dear developers,
> >
> > I am running CS-Rosetta on a protein with a known disulfide pattern and a large proportion of flexible structure. The first models look promising in terms of the recognition of some secondary structure elements (there is a X-Ray structure for the protein), however the overall tertiary structure perdiction is rather poor, which is due to the large flexible links between the secondary structure elements I believe. If I was able to use the known disulfide pattern as restraints the prediction would probably improve significantly. In my current setup the cysteines could not form bonds at all because they are too far from each other. Is there some way to change this? I found there’s a disulfide filter mentioned on the hoempage but could not figure out how I can possibly change its setting.
> >
> > Many thanks and kind regards
> >
> > Baerbel Blaum

[Anonymous]

” Make disulfide bonds with known connectivity,
read connectivity from a file. File format:
i2,1x,i2
Cysteine pairs listed as with cysteine, not by residue #
-find_disulf/-fix_disulfide activate both disulfide

“
The above descriptions are from the README.options_list. For example, you have 4 Cysteine in your protein, and you want to bond the first one and the third one. then you create a file include a line as following:
1 3

that’s it!

> Hi there,
>
> thanks. I found the flag but I have difficulties figuring out what the additional files needs to look like that specifie the cysteine pairs. Basically the documentation mentions two files that need to be added, one for the flag -fix_disulf and a resfile where the cysteines are placed using PIKAA. Additionally I need to turn on the disulfide filter I think. I don’t get the design of the resfile though because it is not clear to me how to use the PIKAA option for disulfides.
>
> CS-Rosetta stands for chemical shift Rosetta. It uses NMR data in addition to sequence similarity to select the fragments that will be used by Rosetta. The step I am struggling with is a pure Rosetta issue I think, so it doesn’t matter that I am using it as part of CS-Rosetta.
>
> Baerbel
>

[kortemme]

Dear Forum readers
I’m trying to run a prediction with the connectivity of disulfide bonds that I know from experimental data. Please be so king to tell me how to do it if any of you know it. another question why do i need a pdb file to start with? (I’ve generated it by running with no fix_disulf first)

The things I´ve tried with no success were:

./rosetta.gcc aa –resfile –find_disulf –fix_disulf connectivity.cst –use_disulf_logfile –nstruct 1000

./rosetta.gcc aa –resfile resfilename.res –fix_disulf –use_disulf_logfile –nstruct 1000

./rosetta.gcc aa –resfile resfilename.res –find_disulf/fix_disulf –use_disulf_logfile –nstruct 1000

Been resfilename.ref generated with makeresfile modifying the Cys with the PIKKA flag

(makeresfile –p –resfile )

Many thanks

[Anonymous]

remove the –find_disulf  in your original command

[Anonymous]

remove the –find_disulf  in your original command

[Anonymous]

remove the –find_disulf  in your original command

[Author]

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