Rosetta 3.5
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Docking Prepack protocol (for Docking)
Author
Robin Thottungal (raugu.nosp@m.st1@.nosp@m.jhu.e.nosp@m.du), Jeffrey Gray (jgray.nosp@m.@jhu.nosp@m..edu)

Metadata

Last edited 7/18/10. Corresponding PI Jeffrey Gray (jgray.nosp@m.@jhu.nosp@m..edu).

Code and Demo

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:

New_Library contains code for this 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:

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

Input Files

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

Options

Flag Description Type

Protocol-Specific Options

-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

-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

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

Tips

Expected Outputs

    1 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).