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Docking Prepack protocol (for Docking)

Metadata

Author: Robin Thottungal (raugust1@jhu.edu), Jeffrey Gray (jgray@jhu.edu)

Last edited 1/25/18. Corresponding PI Jeffrey Gray (jgray@jhu.edu).

Code and Demo

An introductory tutorial on protein-protein docking can be found here.

  • Application source code: rosetta/main/source/src/apps/public/docking/docking_prepack_protocol.cc
  • Main mover source code: rosetta/main/source/src/protocols/docking/DockingPrepackProtocol.cc
  • To see demos of some different use cases see integration tests located in rosetta/main/tests/integration/tests/docking_prepack* (docking_prepack_protocol).

To run docking_prepack, type the following in a commandline:

[path to executable]/docking_prepack_protocol.[platform|linux/mac][compile|gcc/ixx]release –database [path to database] @options

References

We recommend the following articles for further studies of RosettaDock methodology and applications:

  • Gray, J. J.; Moughon, S.; Wang, C.; Schueler-Furman, O.; Kuhlman, B.; Rohl, C. A.; Baker, D., Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology 2003, 331, (1), 281-299.
  • Wang, C., Schueler-Furman, O., Baker, D. (2005). Improved side-chain modeling for protein-protein docking Protein Sci 14, 1328-1339.
  • Chaudhury, S., Berrondo, M., Weitzner, B. D., Muthu, P., Bergman, H., Gray, J. J.; (2011) Benchmarking and analysis of protein docking performance in RosettaDock v3.2. PLoSONE, Accepted for publication.

Application purpose

Use this application to prepare a protein-protein complex for docking via standard docking protocol. In docking, the side chains are only packed at the interface. Running docking prepack protocol ensures that the side chains outside of the docking interface have a low energy conformation which is essential for scoring the decoys.

Algorithm

The docking_prepack algorithm consists of three steps:

  • Move the docking partners out of contact
  • Side chain optimization of the unbound complex
  • Bring the unbound partners back to the original orientation

Note that in a default docking_prepack run, side chain optimization is performed by packing. Commandline options can be supplied to enable additional optimization (sc_min, rt_min).

Modes

  • Docking_Prepack protocol - additional optimization can be achived through the option system.

Input Files

The only required input file is a pdb file containing two proteins with different chain IDs.

Note: An ensemble of input structures can be given using the following flags: -ensemble1 [partner_1_pdb_list] or/and -ensemble2 [partner_2_pdb_list]. These files contain a list of input conformations (in terms of paths to pdbs) of the ensemble. The paths should be as seen from the directory where you run the program and not the directory where partner_1_pdb_list is stored. -ensemble1 corresponds to the list of pdbs of the partner which is written at the top of the input pdb and -ensemble2 to the partner which is at the bottom of the input pdb. Always run this before running the docking protocol for ensembles.

Options

Basic protocol options

Flag Description Type
-docking:partners [P1_P2] Prepacking is done by separating chain P1 and chain P2 String
-docking:partners LH_A (moves chain A around fixed chains L and H) Prepacking is done by separating chain A and LH complex. Note that this will be useful if you are planning to do docking between chain A and LH complex. String
-mp:setup:spanfiles Read in a spanfile for prepacking membrane proteins. Membrane protein is created and partners are translated in the membrane plane. StringVector

optimization Flags

Flag Description Type
-docking::dock_rtmin Does Rotomer trial with side-chain minimization (see Wang, C et al, 2005 in reference) (note: not currently implemented in docking) Boolean
-docking::sc_min Does the side-chain global minimization over all the chi angles after packing. Boolean

Relevant common Rosetta Flags

Flag Description Type
-s 1abc.pdb 1abc.pdb is the pdb file with the protein-protein complex
-database [path to rosetta database folder] The Rosetta database.

Tips

Expected Outputs

One PDB file for each structure generated and a 1 scorefile for each run with scoring and name information for each structure generated.

New things since last release

Supports the modern job distributor (jd2).