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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

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:

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:

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.