What is the general protocol for antibody-antigen docking without the native antibody-antigen structures?
Submitted by Sunyp_IM on Sun, 2017-08-13 05:42
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Docking
Issues with residues and structure changing with FlexPepDock; is this normal?
Submitted by rnelson on Tue, 2017-08-08 10:06
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Docking
This is probably a silly question so I apologize if so, but recently lab has been investigating some novel interaction sites between a protein and peptide based off of recent crosslinking and IP data. I created some pdb files of the protein and the peptide aligned at the various novel and established crosslinking sites and submitted them to FlexPepDock to see if the models were reasonable.
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MPdocking I_sc
Submitted by jrcf on Mon, 2017-07-31 16:10
Category:
Docking
Hi guys...
I'm run the protocol MPDocking, and the result I had from the I_sc was confused.
I read here (https://www.rosettacommons.org/content/score-use-picking-top-docking-solutions) a good score is between -5 and -10, but the number is very high.
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Rosie Docking Server-Energy function
Submitted by jsv on Fri, 2017-07-21 08:26
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SNUGDOCK
Submitted by adva on Sun, 2017-07-16 00:49
Category:
Docking
Hello,
I am trying to run SnugDock locally, and I follow the well explained demo. I noticed that makefab.pl script is missing. It should be in the demo / rosettascripts directory but its not there. Also, there is a link in the README.md file but its blocked by a usename and password....
Can anyone help?
Thanks,
Adva
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SNUGDOCK
Submitted by adva on Sun, 2017-07-16 00:46
Category:
Docking
Hello,
I tried running snugdock on ROSIE. The run finished and when I downloaded the output files from the server, I got this messge in the output.json file:
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Some problems with the "advanced protein-protein docking" tutorial
Submitted by Sunyp_IM on Tue, 2017-06-27 09:33
Category:
Docking
I am studying the Rosetta "advanced protein-protein docking" tutorial (https://www.rosettacommons.org/demos/latest/tutorials/advanced_protein-protein_docking/advanced_protein-protein_docking_tutorial), but I find some confusing problems with it.
Problem 1
The input file pdb file for the docking command:
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Problems with "pdb_renumber.py" in tutorial Advanced Protein-Protein Docking
Submitted by Sunyp_IM on Sun, 2017-06-25 02:40
Category:
Docking
Dear all,
I am learning the advanced "protein-protein docking" part of the Rosetta about the docking of HA and antibody. When I input the following command in this tutorial:
$ROSETTA_TOOLS/protein_tools/scripts/pdb_renumber.py --norestart input_files/3GBM_AB.pdb input_files/3gbm_HA.pdb
I get the following error message:
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Error Interface analyser
Submitted by jrcf on Thu, 2017-06-22 12:55
Category:
Docking
Hi people,
I'm trying to use the interfaceAnalyzer, but this error is showing.
This is the script I run
obs. I don't know why the output score doesn't make.
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Adding water interactions when docking a ligand with Rosetta 3.7.
Submitted by brspurri on Thu, 2017-06-01 09:37
Category:
Docking
I am using RosettaScripts to dock a ligand, and I would like to include several - known - key water interactions.
I found a demo somewhere (RosettaCon?) that showed this is possible, but I it looked like the xml was designed for a version well before Rosetta 3.7. From reading the Scripts docs, it looks like including the term minimize_water=true to the <MOVEMAP_BUILDER /> element should handle the water interactions.
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