protein protein interaction design

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    • May 15, 2019 at 1:13 pm #3146
      Anonymous

         

        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?

         

         

      • May 15, 2019 at 4:07 pm #14730
        Anonymous

          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

          • May 15, 2019 at 5:34 pm #14731
            Anonymous

              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?

               

               

               

               

            • May 15, 2019 at 10:40 pm #14733
              Anonymous

                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.

                 

                 

                 

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