<!-- --- title: Docking Prepack Protocol -->Docking Prepack protocol (for Docking)
Metadata
Author: Robin Thottungal (raugust1@jhu.edu), Jeffrey Gray (jgray@jhu.edu)
Last edited 7/18/10. Corresponding PI Jeffrey Gray (jgray@jhu.edu).
Code and Demo
- Application source code:
rosetta/rosetta_source/src/apps/public/docking/docking_prepack_protocol.cc - Main mover source code:
rosetta/rosetta_source/src/protocols/docking/DockingPrepackProtocol.cc - To see demos of some different use cases see integration tests located in
rosetta/rosetta_tests/integration/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.
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 usefull if you are planning to do docking between chain A and LH complex. | String |
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).