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Using pyrosetta to generate quaternary structure of protein

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Using pyrosetta to generate quaternary structure of protein
#1
Hello,
Assume I have two proteins that have known tertiary structures. Is there a way that I can load these two proteins in pyrosetta, make some restraints between residues of these two proteins, and then use gradient descent to minimize the cost function in order to predict the interaction (based on constructed constraints) between these two proteins? If yes, could you please explain or provide me with some resources? I'm completely new to pyrosetta.
 
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Thu, 2020-11-19 17:35
nasim.soltani58

Look into protein protein docking.  I would use regular Rosetta for this on a compute cluster.  https://www.rosettacommons.org/docs/latest/application_documentation/docking/docking-protocol

Thu, 2020-11-19 18:34
jadolfbr

Thank you very much. But, the link that you sent is not with gradient descent, I think the algorithm is Monte carlo, right?

Thu, 2020-11-19 21:08
nasim.soltani58

If they are already at the binding site in the crystal structure, you can use the MinMover or FastRelax to miniminize, or minimize/pack side chains.  Contraints are also available in what ever way you want to. Some of those are covered in the PyRosetta notebooks tutorials: https://github.com/RosettaCommons/PyRosetta.notebooks  If they are monomers and you are trying to get the best orientation between them, you want docking with constraints.  

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

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

Fri, 2020-11-20 07:55
jadolfbr

Thank you very much. I will try to do it and then update it, but because I'm new it might take some time.

Thank you once again.

Fri, 2020-11-20 11:30
nasim.soltani58