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protein protein interaction design

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protein protein interaction design
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Hello

I have docked two proteins  and Now I am going to design the binding interface of one of them while fix everything in the other. I mean I want to do protein protein interaction design. which part of rosetta would be for this job?? is it fixbb?

 

 

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Wed, 2019-05-15 06:13
Negarsardar

Hi!

I would use RosettaScripts. Your best bet is to find an example XML that does approximatly what you want and then adapt it to the specifics. 

(Disclamer: I'm not doing one-sided protein interface design:)

 

Best,

Ajasja

Wed, 2019-05-15 09:07
ajasja

the problem is Im new to work with rosetta and bioinformatic, so I dont know How I should find rosetta script and use it. I want to know  is it really wrong choice to use fix bb for this purpose?

 

 

 

 

Wed, 2019-05-15 10:34
Negarsardar

That's a problem. You'll have the best sucess if somebody locally can help you. 

However just googling for "Rosetta interface protein design" gives a usefull second hit https://www.rosettacommons.org/demos/latest/public/rosetta_scripts_pp-interfaceredesign/README.

This should get you started.

 

 

 

Wed, 2019-05-15 15:40
ajasja