Structure prediction using true distance and angle constraint

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    • August 21, 2019 at 9:29 am #3268
      Anonymous

        Hello,

        I wonder if naive protein structure can be predicted by using true distance and angle constraints.

        If we can do that, how do we choose rosetta applications and parameters?

      • August 21, 2019 at 10:29 pm #14887
        Anonymous

          https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/HybridizeMover

          https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/abinitio-relax

          https://www.rosettacommons.org/docs/latest/rosetta_basics/file_types/constraint-file

          • August 27, 2019 at 8:21 am #14914
            Anonymous

              Hi, smlewis. Thanks for your reply.

              I found that HybridizeMover requires a template. But I have no template for builting model.

              I have tried to use abinitio-relax for structural prediction and added experimental constraint as follows:

              AtomPair CB 63 CA 65 FLAT_HARMONIC 3.47 1.0 0.50

              AtomPair CB 67 CB 69 FLAT_HARMONIC 6.47 1.0 0.50

              ….

              Dihedral C 3 N 4 CA 4 C 4 CIRCULARHARMONIC 1.71 0.50

              Dihedral N 4 CA 4 C 4 N 5 CIRCULARHARMONIC -2.33 0.50

              Dihedral C 4 N 5 CA 5 C 5 CIRCULARHARMONIC -1.72 0.50

              ….

              But the result is very different from the naive structure. I’m wondering what went wrong.

              Any help would be appreciated.

            • September 16, 2019 at 9:10 pm #14966
              Anonymous

                There are a thousand places this could go wrong.  I don’t actually know what is wrong – particularly I cannot parse “the result is very different from the naive structure”. If you mean naive as constraint-free: I would expect that the constrained result should be very different, that’s the point of constraints.  If you meant ‘native’, then I don’t know why you don’t have a template for hybridize.

                If you are doing effectively ab initio with constraints, I would guess the constraints aren’t strong enough during the early stages; perhaps they are not on at all if they are not active in the scorefunction.  I can guess another dozen things that might be wrong but I don’t have enough data to tell.

                You should probably re-ask this in a new thread; it’s easier to get attention to unanswered posts and I clearly don’t know enough about what you are trying to do to help.

              • September 27, 2019 at 1:52 am #14989
                Anonymous

                  We have increased the weight of the constraint and this problem is solved.

                  Thank you very much!

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