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Docking

How to extract antibody from a set of pdb file may may contain antigen?

Category: 
Docking

Dear all,

I have a set of pdb structure files that contain antibodies but may or may not contain antigens. I want to extract only the antibodies from each of these structures. Do anyone know how to do it?

Best regards,

Yeping Sun 

Post Situation: 

keep ATP in the kinase-peptide structure while docking

Category: 
Docking

Hi,

i'm trying to dock a peptide into kinase. It's very important to keep ATP molecule in the kinase ortherwise some peptide simulation model will occupy ATP's position.

But the flexpepdock will remove all not aminoacid molecules. I was wondering is there any way I can do that ? Or an alternative module on Rosetta? 

Thank you!

Post Situation: 

Error: Could not find scorefxns and name score12 in Datamap in rosetta_bin_linux_2017.39.59729_bundle

Category: 
Docking

Hi everyone,

I had to reinstall newest rosetta (rosetta_bin_linux_2017.39.59729_bundle), but after successful installation and compilation, when I want to get docking using following commands and script:; 

 

 ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/linux_programs/rosetta_bin_linux_2017.39.59729_bundle/main/database/ -nstruct 200 -s 1czH_1czW.pdb -ex1 -ex2 -parser:protocol  docking_stubs.xml

 

Post Situation: 

How to make a resfile

Category: 
Docking

Hello,

I am new to using Rosetta. I would like to make a res file to mutate through all 20 amino acids in a Protein-protein interface and predict binding energy using RosettaDesign.  This might be a stupid question but how to you make a resfile? Do you write it in text edit? Is the file extention .res?

I have found the refile syntax page from Rosettas website but it does not say where you type any of the commands into or how to save it.

Post Situation: 

Ligand docking cannot open the protein file

Category: 
Docking

Hi there!

I follow the ligand docking tutorial from here: https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/ligand_docking_tutorial

When I get to point 6 and try to run docking protocol via ./rosetta_scripts.linuxgccrelease @options it says ERROR: Cannot open file "3PBL_ETQ.pdb"

How can I check the particular path to the file and correct, if needed?

Thanks in advance!

 

Post Situation: 

Dock two domains using topology broker

Category: 
Docking

Hi,

I have two domains that are asymmetric and I want to dock them using topology broker (asymmetric fold and dock like operation). Below is the full description of my problem:

1. I have pdbs for two domains that I want to dock. Domain1 has 3 chains and domain2 and 1 chain

Post Situation: 

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