Using GlycanDock and the Antibody Affinity Maturation protocol.
Hello, I have been reviewing the docking movers to perform both types, global and local. I have been testing them for a while now and with the active options to perform the global docking first, very little movement and exploration of the protein is observed in the output, the disturbances are practically local instead of global, this occurs both for DockingProtocol Mover and for Docking Mover. Would I have to first use DockingInitialPerturbation Mover or else use global docking flags and then use DockingProtocol or Docking for local?
I would like to dock unknown chemical into PDB which have HEM as a cofactor
But I want to fix the HEM molecule fixed during docking with constraint statement below
<ResidueName name="HEM" residue_names="HEM" residue_name3="HEM" />
Recently I'm trying to do protein-ligand docking with rosetta scripting interface
what I want to do is to incorporate charge grid in rosetta script xml file as shown below
<SCORINGGRIDS ligand_chain="X" width="25" name="charge">
<ChargeGrid grid_name="charge" weight="1.0"/>
I am writing a python script that will do docking for my antibody-antigen samples, however, I could not find any SnugDock code examples with pyrosetta. Could you please give at least one?
A general question would be whether there is a docking protocol for HDX-MS. Can I get a share?
Then I have two questions to the paper "Robustification of RosettaAntibody and Rosetta SnugDock" from Gray's group:
Is it possible to perform global ligand docking with Rosetta script not PyRosetta?
I found the tutorial for global ligand docking in PyRosetta. ( https://nbviewer.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.01-Ligand-Docking-XMLObjects.ipynb )
But, I could not find any explicit example for global ligand docking with only Rosetta script.
I would like to dock a small protein on a metal surface. It may be similar simulations which has done by Jeff Gray's group. But I found the code in surface_docking was written for pyrosetta 2 based on python 2.x . I have tried to transform the script to python3.. However, unknown errors appeared all the time.
Can anyone tell me how to use these code in Pyrosetta4 (python3) or provide any detailed tutorial for surface_docking in Pyrosetta4?
Thanks very much!
I want to get a series of enzyme-substrate binding pose in one step of my research, but I met some questions: