autoNOE peak lists

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    • August 6, 2015 at 1:15 pm #2244
      Anonymous

        Hello.
        I am using autoNOE and RASREC Rosetta to try to calculate a protein structure using sparse NMR NOESY data. I am wondering if there is a way I can input a partially (manually) assigned NOE peak list into the autoNOE setup, not just a completely unassigned list. I know I can give RASREC cyana-style upl constraints, but that’s not what I’m looking for. I’d like to see if I can improve the accuracy of the autoNOE sampling by giving it a few manually-determined, unambiguous noe assignments, I just don’t know how to properly format that input peak list.
        Thank you!

      • August 19, 2015 at 1:25 am #11154
        Anonymous

          Hi,

          Yes, you can combine autoNOE/RASREC with conventional constraints to boost sampling towards conformations that will allow you to assign more. simply use the same options for cyan upl constraints together with the autoNOE options while setting up/running the calculations.

          I more detailed example is detailed here:
          http://csrosetta.chemistry.ucsc.edu/node/1357

          I hope this helps,
          Nik

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