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Negative Design

Submitted by rbjacob on Thu, 2018-10-11 09:18
Category: 
Docking

Hello,

 

I am trying to come up with a protocol (xml script) that will allow me to perform positive design for one substrate and negative design for the inhibitor. Our goal is to create a protein that maintains functionality and is resistant to the inhibitor.

I am open to any suggestion. I have not been able to find any documentation on how to perform docking_design in this manner.

Thanks

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Rosetta 3 - Applications

RosettaAntibody core.pose.util error

Submitted by rishibedi on Fri, 2018-10-05 01:31
Category: 
Structure prediction

Hi,

I'm using Rosetta 3.8 on Linux (rosetta_bin_linux_2017.08.59291_bundle; pre-compiled binaries). I'm trying to use the RosettaAntibody3 workflow as documented here, but am running into the following error when I run the sample command (using the sample antibody sequences in antibody_chains.fasta as given in the workflow):

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Rosetta 3 - Applications

rosetta backrub

Submitted by ladimafakher on Thu, 2018-10-04 08:01
Category: 
Design

Hello

I want to use Rosetta backrub for peptide design. by I faced an error that I think it caused to incompatible .py and .sh files and Rosetta 3.9 2018 version. I searched a lot on Rosetta website to find out any example of .py and .sh file that they need for running Rosetta Backrub. my error was ERROR: unable to open MM atom type  set file:/home/nanobio/amin/rosetta_database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt ERRoR: Exit from: src/core/chemical/MMAtomTypeSet.cc line 64".

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Rosetta 3 - Applications

How to define the surface (???.surf) for surface_docking?

Submitted by Anpu on Thu, 2018-09-27 07:34
Category: 
Docking

Dear Rosetta Team,

When docking a protein with a solid surface, Rosetta will need a .surf file; Any one can tell me how to setup/edit a .surf file for a certain solid surface (a .pdb file) for surface docking? In the demo example for the calcite.surf, there is not detailed instruction to tell how to do it? Only three lines, with likely X,y,z in the calcite.surf file. I dont know what they are representing for a solid surface?

Thanks

An Pu

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Rosetta 3 - General

problem installing latest version of rosetta

Submitted by anilkumarnaik on Mon, 2018-09-24 21:19
Category: 
Compilation

Unable to build latest version of rosseta at below Linux workstation. Errors for python version not compatibile. Kindly let us know the rosetta version compatibile with below system specs? Also share the link to download the older version of rossetta software. 

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Rosetta 3 - Build/Install

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