Docking Prepack protocol (for Docking)
Last edited 1/25/18. Corresponding PI Jeffrey Gray (firstname.lastname@example.org).
An introductory tutorial on protein-protein docking can be found here.
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
We recommend the following articles for further studies of RosettaDock methodology and applications:
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.
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).
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.
|-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|
|-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|
|-s 1abc.pdb||1abc.pdb is the pdb file with the protein-protein complex|
|-database [path to rosetta database folder]||The Rosetta database.|
One PDB file for each structure generated and a 1 scorefile for each run with scoring and name information for each structure generated.
Supports the modern job distributor (jd2).