Protein Structure Prediction

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    • April 5, 2012 at 7:36 pm #1227
      Anonymous

        Hi everybody,
        I am trying to use pyrosetta to make a prediction of the structure of a protein. I am new with python and pyrosetta and I am having difficulties. Anyone could tell me the best way of doing it? Which scripts should I use first,..? My idea was using an script to make a first structure calculation in centroid mode, and afterwards doing a refinement, loop modeling, side-chain packling and so on.
        Anyone has a simple scrits to do the first taks? the protein folding? I ahve found one but it uses a pdb, I just have a sequence.
        Thanks,
        Nuria

      • April 5, 2012 at 8:08 pm #6929
        Anonymous

          Any reason you are not using the pre-existing C++ applications for this?

        • April 5, 2012 at 8:27 pm #6931
          Anonymous

            Steven is right, this is what I tried to do during my rotation a few years ago, and I should have just used the C++ applications. I wasted a decent amount of time and a potential paper…. But, I learned python and parts of pyrosetta, so that was useful.

            Anyhow, I am not sure if Abrelax works in PyRosetta. After some digging, there is an AbrelaxApplication object exposed. You can make one using x = AbrelaxApplication(). However, I know nothing about it, and wouldn’t recommend trying to get it to work. Best bet is to use Abinitio in main Rosetta, cluster the 10-30 thousand models using the program calibur, and then take the top cluster or two and loading that into pyrosetta or in main rosetta to do loop modeling / further repacking / design/ etc.

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