how build (N-terminal 17 residues) structre /fragment file generation

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    • July 28, 2016 at 6:56 am #2476
      Anonymous

        Greetings, 

        1) How to generate the n-terminal region say 17 residues (loop only, no homologs structure available in pblast )

        2) Entire protein sequence structure got Robetta n-Terminal is only loop in MD run it’s not converging. 

        Accordingly plan to do loop model is that way good way? or any other Rosetta application will help in is this situations

        Kindly let me know  

        Awaiting your replay

      • July 28, 2016 at 2:21 pm #11760
        Anonymous

          “2) Entire protein sequence structure got Robetta n-Terminal is only loop in MD run it’s not converging. “

          Do you have any reason to beleive this region IS firmly structured?  If it’s just a flexible tail, then MD won’t converge and Rosetta won’t either; it’s not converged in real physics.

          If you expect it to be tightly structured, continue with homology modeling or hybridize via Robetta as normal.

          If you don’t expect regular structure, and are just interested in a population of possible structures / determining the envelope of space the tail could occupy, try FloppyTail.  Note the C_root option if you have an N-terminal tail.  https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/floppy-tail

        • July 29, 2016 at 8:14 am #11761
          Anonymous

            Thank you for reply,

            Yes, am expecting structure  in experimental reported (“not structural studies”) N-terminal (“17 residues”) and C-terminal (with help of Abinitio relax got structure “75 residues”) are interacting with some protein (in crucial way).

            May correct or not, don’t know am believe in loop structure may not get proper interactions ? 

            Thank you

          • July 29, 2016 at 2:43 pm #11762
            Anonymous

              You can try loop modeling, certainly.  I think the CCD modes will let you model termini (I’m not sure).  I’m pretty sure the KIC modes won’t let you model termini.  If the termini are well-structured, then homology modeling or loop modeling have a good chance of finding the correct structure.  If the terminus isn’t actually well structured in solution, then Rosetta isn’t going to be able to find the “one structure” as it doesn’t exist anyway.

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