Give preference to native residue during fixed backbone designing

This topic has 6 replies, 3 voices, and was last updated 8 years, 5 months ago by Anonymous.

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- April 4, 2016 at 7:43 pm #2405
  Anonymous
  Hi,
  
  I want to do fixed back-bone design. Rosetta output gives me a lot of mutation. I want to limit the numbers. I donot want mutations that marginally stabilizes the protein. Is there any way to tell to software to prefer the native aminoacid.
  
  Thanks a lot
- April 8, 2016 at 3:49 pm #11503
  Anonymous
  How are you doing your mutations?
  
  This is not so easy to do for the fixbb application, but it is quite straightforward through RosettaScripts. See the https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/FavorNativeResidueMover for a simple FavorNativeResidue approach, and https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/FavorSequenceProfileMover for a more flexible approach that allows you to give partial bonuses for similar residues (e.g. SER and THR).
  
  Also, you’ll probably want to read Nivon et al. “Automating human intuition for protein design”: http://dx.doi.org/10.1002/prot.24463 which does pretty much exactly what you’re talking about.
- April 8, 2016 at 4:29 pm #11504
  Anonymous
  Dear Tushar,
  
  In the old Rosetta++ days, there was an option “-favor_native_residue” that did
  what you want. Currently, it does not work with the fixbb application. This is
  a known bug https://carbon.structbio.vanderbilt.edu/mantisbt/view.php?id=160
  
  However, there is a work-around. Instead of the fixbb application, you can use
  rosettascripts as documented here:
  https://www.rosettacommons.org/demos/latest/public/favor_native_residue/README
  
  Look at these files in your rosetta distribution for an example you can adapt:
  $ROSETTA_DIR/demos/public/favor_native_residue/
  
  Good luck!
- April 11, 2016 at 6:06 am #11508
  Anonymous
  Hi rmoretti,
  
  Hi sheehajh,
  
  Thanks for your valuable advice. Initially I was following the paper incorrectly. Now my problem got resolved.
- April 10, 2016 at 5:26 pm #11505
  Anonymous
  Hi rmoretti,
  
  Hi sheehajh,
  
  Thanks for your valuable advice. I went through the above link and the paper regarding Rosetta script. I could able to run the sript but the problem is it didn’t consider the res file which I have mentioned in command line. When I added “<ReadResfile name = rrf filename = myresfile.res />” line as recommended in the paper I got an error saying “ReadRes file is not known to the MoverFactory “. May I know how to use resfile (or provide the same information) while using rosetta script.
  
  Thanks a lot.
- April 10, 2016 at 5:27 pm #11506
  Anonymous
  Hi rmoretti,
  
  Hi sheehajh,
  
  Thanks for your valuable advice. I went through the above link and the paper regarding Rosetta script. I could able to run the sript but the problem is it didn’t consider the res file which I have mentioned in command line. When I added “<ReadResfile name = rrf filename = myresfile.res />” line as recommended in the paper I got an error saying “ReadRes file is not known to the MoverFactory “. May I know how to use resfile (or provide the same information) while using rosetta script.
  
  Thanks a lot.
- April 28, 2016 at 10:19 pm #11538
  Anonymous
  To clarify for possible future readers, the issue is that the ReadResfile tag needs to go into the TaskOperations section, rather than the Movers section. (ReadResfile isn’t known to the MoverFactory because it’s a TaskOperation.)
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