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Protein Structure Prediction

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Protein Structure Prediction

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.

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Thu, 2012-04-05 12:36

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

Thu, 2012-04-05 13:08

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.

Thu, 2012-04-05 13:27