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RosettaCommons / PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
https://rosettacommons.github.io/PyRosetta.notebooks/
MIT License
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Docking Protocols #77

Closed LivC193 closed 2 years ago

LivC193 commented 2 years ago

Dear Madam/Sir,

I am trying to understand the docking classes outlined here.

How can I find out which classes use high resolution docking (full atomistic) and which use low resolution (centroid)? I am particularly interested in DockMCMProtocol and DockingEnsemble.

Furthermore I am interested in performing Flexible Docking using the ensemble1 and ensemble2 flags, is DockingProtocol able to do this? If so does it take care of the prepack step as well?

jadolfbr commented 2 years ago

Low and High res dock are covered in the docking chapter: https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/07.02-Docking-Moves-in-Rosetta.ipynb