Modeling only part of the protein structure using ROSETTA

[Anonymous]

Hello all,
We are trying to calculate a protein ensemble using CS-ROSETTA. We have reasonable evidences to believe that only part of the protein (C terminal part) undergoes conformational change at the condition while the rest (N terminal part) remains as a similar structure that we have already known. The protein has 146 aa, we are just wondering is there a way for ROSETTA to “Freeze” part of the protein and only do the calculation on the other part? Thanks in advance for help.

Qiong

[Anonymous]

The short answer is: find the MoveMap in the protocol, and change it so that it only allows the desired positions to move.

What protocol are you using?

See the thread “modeling loops between domains” in this thread for details on MoveMap modification in relax mode (same changes to different code for other modes).

[Anonymous]

Thank you so much for your reply. I am reading the thread and trying to get better understanding. The program I am using is CS-ROSETTA, I believe it is RosettaAbinitio routine. I will follow your instruction and hopefully get it to work.

Qiong
> The short answer is: find the MoveMap in the protocol, and change it so that it only allows the desired positions to move.
>
> What protocol are you using?
>
> See the thread “modeling loops between domains” in this thread for details on MoveMap modification in relax mode (same changes to different code for other modes).

[Anonymous]

> Hello all,
> We are trying to calculate a protein ensemble using CS-ROSETTA. We have reasonable evidences to believe that only part of the protein (C terminal part) undergoes conformational change at the condition while the rest (N terminal part) remains as a similar structure that we have already known. The protein has 146 aa, we are just wondering is there a way for ROSETTA to “Freeze” part of the protein and only do the calculation on the other part? Thanks in advance for help.
>
> Qiong

[Anonymous]

Hello all,

I’m trying to build up just one part of my protein giving to rosetta a pdb file with the rest of the structure that would have to be frozen…..How can I do this using Abinitio folding mode? Do I have to change the code of the Abinitio mode?
Did you manage to do this?

Thanks in advance for help

Cristina

> Hello all,
> We are trying to calculate a protein ensemble using CS-ROSETTA. We have reasonable evidences to believe that only part of the protein (C terminal part) undergoes conformational change at the condition while the rest (N terminal part) remains as a similar structure that we have already known. The protein has 146 aa, we are just wondering is there a way for ROSETTA to “Freeze” part of the protein and only do the calculation on the other part? Thanks in advance for help.
>
> Qiong

[Anonymous]

The abinitio application supports partial starting structures. Run the abinitio application with the -help option; most of the options that pop up with “native” in them address the problem you describe. (No, I don’t know how to use them).

[Author]

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