Documentation for the oop_design application

Author

Kevin Drew, kdrew.nosp@m.@nyu.nosp@m..edu

Metadata

Last updated November 30, 2012;

Code and Demo

• Application source code: rosetta/rosetta_source/src/apps/public/noncanonical_backbones/oop_design.cc
• Mover source code: rosetta/rosetta_source/src/protocols/simple_moves/oop/OopRandomSmallMover.cc
• Mover source code: rosetta/rosetta_source/src/protocols/simple_moves/oop/OopRandomPuckMover.cc
• For a demonstration of a basic run see integration folder (rosetta/rosetta_tests/integration/tests/oop_design/) and demo folder (rosetta/rosetta_demos/oop_design).
  

Documentation for the oop_design application

The main references for the oop_design app are to be published in the PlosOne 2013 Rosetta Special Collection

New_Library contains code for this purpose

Oligooxopiperazines (oop) are a scaffold peptidomimetic (4-6 residues in length with cyclized backbones every two residues) that mimics the i, i+4, i+7 residues of an alpha helix. Many protein interaction interfaces involve helices and there is interest in using oops for protein interaction inhibitors. The rational design of oops using the oop_design app attempts to find high affinity binders to target proteins.

Algorithm

1. Pertubation phase: rigid body movement of oop wrt target, oop small moves to oop ring conformation, oop puck move to change oop ring pucker, small moves to ring linkers
   
2. Design phase: design user specified residues on oop scaffold and minimize
   
3. Repeat 10x

Input Files

oop_design requires the following inputs:

• Starting structure:
  The starting structure should have two chains, where the first should be the target protein and the second the oop scaffold (see demo inputs for example). The starting conformation should be close to a plausible binding mode because the oop_design app does not do large pertubations. The starting structure should also be refined prior to input where the recommended procedure is to do relax with constraints (reference).

Options

I. Common oop_design flags:

   Flag

   
   

   Description

   
   

   Type

   
   

   Default

   
  
 



   -oop_design_positions
  
 

  positions on oop chain to be designed
  
 

   list of numbers [ex. 1 2 3 6]
  
 

  None, only repack, no design
  




 -pert_num
 
  

  number of pertubations made during pertubation phase
  
 

   integer
  
  

  10
  
 



 -design_loop_num
 
 

  number of pertubation + design cycles
 
 

  integer
 
 

   10
 
 

II. Relevant Common Rosetta flags

More information on common Rosetta flags can be found in the relevant rosetta manual pages). In particular, flags related to the job-distributor (jd2), scoring function, constraint files and packing resfiles are identical to those in any other Rosetta protocol).

        Flag
        
        

          Description
        
      
      


          -in::file::s
          


          Or
          


          -in:file:silent
        
        

          Specify starting structure
          (in::file::s for PDB format, in:file:silent for silent file
          format).
        
      
      


          -in::file::silent_struct_type  


          -out::file::silent_struct_type
        
        

          Format of silent file to be read
          in/out. For silent output, use the binary file type since
          other types may not support ideal form
        
      
      


          -nstruct
        
        

          Number of models to create in the
          simulation
        
      
      


          -use_input_sc
        
        

          Include rotamer conformations from the input structure
          during side-chain repacking. Unlike the -unboundrot flag,
          not all rotamers from the input structure are added each
          time to the rotamer library, only those conformations accepted
          at the end of each round are kept and the remaining
          conformations are lost.
        
      
      


          -ex1/-ex1aro -ex2/-ex2aro -ex3 -ex4
        
        

          Adding extra side-chain rotamers
        
      
      


          -database
        
        

          The Rosetta database
        
      
      


          -include_patches
        
        

          Turn on patch files which are off by default.  Turning on patches/oop_pre.txt and patches/oop_post.txt is a requirement for oop applications. 
        
      
     
  

Tips

Example runs

generate 1000 (or more) models

 oop_design.{ext}
-database ${rosetta_db} -include_patches patches/oop_pre.txt patches/oop_post.txt -s start.pdb -nstruct 1000 -oop_design_positions 1 2 3 4 -pert_num 100 -design_loop_num 10

Sort models by total score, take top 5%, sort by REPACK_ENERGY_DIFF. Inspect top models.

Limitations:

• Start with good binding mode:
  This application does not do large pertubations and therefore only minimally explores the space around the input structure. Use experimental evidience, a full docking app or estimate the binding mode by hotspot residues of native complex.

• Target model:
  This application assumes the backbone of the target structure is in a fixed conformation and does not do flexible backbone moves.

• Oop length:
  This application has only been tested for oop dimers (4 residues). Although untested, there is no obvious reason why an oop trimer or an extended oop (ex. oop dimer with n-term or c-term additional residues would not work.

• Typical running time:
  With default settings and a typical input structure (~ 100 residues), a single model is estimated around 15 seconds. For a recommended 1000x models, the runtime should be around < 25 mins.

• Multichain receptors:
  This app currently supports only the use of single-chain targets. If you want to use a multichain target, you may be able to get away with hacking your input PDB to re-label all target chains as one big chain (removing termini atoms and TER cards). Renumbering is necessary only to resolve numbering conflicts.

Expected Outputs

The output of a oop_design run is a score file (score.sc by default) and k model structures (as specified by the -nstruct flag and the other common Rosetta input and output flags). The score of each model is the second column of the score file.

Post Processing

Model selection should be made based on sorting by total score, take top 5% and sort by REPACK_ENERGY_DIFF in the score file.