H3 modelling scoring function

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- December 28, 2017 at 7:10 am #2823
  Anonymous
  Dear all,
  
  Let’s suppose we have the following situation:
  
  I have an antibody structure generated by the ‘antibody.linuxgccrelease’ (i.e. no H3 optimization yet, just grafting)
  
  Is it possible to score it in a similar fashion as the ‘antibody_H3.linuxgccrelease’ application does? I mean to score it without, H3 optimization whatsoever?
  
  I saw that in the scoring file of a H3 optimization run we can find different terms than in a normal Talaris2014 relaxing/scoring:
  
  CDR_SASA CDR_SASA_HP CDR_charge H1_RMS H2_RMS H3_RMS L1_RMS L2_RMS L3_RMS VL_VH_distance …. etc.
  
  Any help will be greatly appreciated.
  
  Thank you,
  
  Andrei
- January 3, 2018 at 4:16 pm #13975
  Anonymous
  Hey Andrei,
  
  You can get approximate RMSDs by running, “antibody_H3.linuxgccrelease -antibody:model_h3 false -antibody:snugfit false -antibody:refine_h3 false -s model.pdb -native crystal.pdb”. I say approximately becuase there are a few steps which cannot be skip in the antibody_H3 executable by setting options alone, so there will be a little motion (~0.1 A RMSD). Alterntively, I can provide a Python script that use PyRosetta to calculate loop RMSDs.
  
  To get metrics regarding light–heavy chain orientation, please use the packing_angle.linuxgccrelease application. I believe all it requires is an input structure with “-s input.pdb”.
  
  Best,
  
  Jeliazko
- January 9, 2018 at 7:49 am #13982
  Anonymous
  Dear Jeliazko,
  
  Many thanks for your reply! It works just fine. We already have a script in VMD to calculate the H3 RMSD and local fitting.
  
  Do you think that it make any sense to calculate the sum of the scores for the H3 residues and use it instead of total score?
  
  Thanks.
  
  All the best,
  
  Andrei
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