Documentation for Docking protocol and application

Author:: Brian Weitzner (brian.weitzner@jhu.edu), Monica Berrondo (mberron1@jhu.edu), Krishna Kilambi (kkpraneeth@jhu.edu), Robin Thottungal (raugust1@jhu.edu), Sidhartha Chaudhury (sidc@jhu.edu), Chu Wang (chuwang@gmail.com), Jeffrey Gray (jgray@jhu.edu)

Metadata

Last edited 9/22/10. Corresponding PI Jeffrey Gray (jgray@jhu.edu).

Code and Demo

Application source code: src/apps/public/docking/docking_protocol.cc
Main mover source code: src/protocols/docking/DockingProtocol.cc
To see demos of some different use cases see integration tests located in src/test/integration/docking* (docking_full_protocol, docking_local_refine, docking_local_refine_min, docking_low_res).

To run docking, type the following in a commandline:

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

Note: these demos will only generate one decoy. To generate a large number of decoys you will need to add –nstruct N (where N is the number of decoys to build) to the list of flags.

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.
Gray, J. J.; Moughon, S. E.; Kortemme, T.; Schueler-Furman, O.; Misura, K. M.; Morozov, A. V.; Baker, D., Protein-protein docking predictions for the CAPRI experiment. Proteins 2003, 52, (1), 118-22.
Wang, C., Schueler-Furman, O., Baker, D. (2005). Improved side-chain modeling for protein-protein docking Protein Sci 14, 1328-1339.
Schueler-Furman, O.; Wang, C.; Baker, D., Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005, 60, (2), 187-94.
Wang, C., Bradley, P. and Baker, D. (2007) Protein-protein docking with backbone flexibility. Journal of Molecular Biology, 2007 Oct 19;373(2):503-19. Epub 2007 Aug 2.

Purpose

Determine the structure of protein-protein complexes by using rigid body perturbations of the protein chains.

The docking algorithm consists of a low-resolution mode in which the side chains are represented as a single pseudo-atom. The first step in low-resolution mode is to make a large perturbation in order to generate a unique starting structure for the docked conformation. This mode makes large perturbations in order to rigorously sample the translational and rotational space for binding-competent conformations. The best scoring conformation is converted to an all-atom representation and then undergoes small rigid body perturbations as well as optional backbone minimization and side chain optimization. The lowest scoring conformation is written to a pdb file and the score information for each generated structure is written to a single scorefile.

Modes

Full protocol - The full protocol involved first exploring the conformational space of the partners through a low resolution search followed by all-atom refinement with a local refinement through a Monte Carlo Minimization algorithm.
Low resolution docking - The protein is represented as backbone plus centroid representation of sidechains, i.e. the sidechain is represented as one giant atom to save CPU time. In this stage RosettaDock attempts to find the rough orientation of the docking partners for the high-resolution search.
Local refinement - All atoms in the protein are represented, and the position found in the low-resolution search is optimized. Rigid body MCM is alternated with sidechain repacking so that the sidechains can adjust to a new, more favorable orientation and vice versa. The high-resolution stage uses up the most CPU time of Rosetta.
Local refinement minimization - Similar to Local refinement, all atoms in the protein are represented. A single run of minimization is done to minimize the energy of the rigid body position. Minimization is followed by side-chain packing.

Input Files

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

Options

Flag

Description

Type

Basic protocol options

-partners [P1_P2]
-partners A_B (moves chain B around chain A)

-partners LH_A (moves chain A around fixed chains L and H)

Defines docking partners by chain ID for multichain docking

String

Perturbation Flags

-randomize1	Randomize the orientation of the first docking partner. (Only works with 2 partner docking).	Boolean
-randomize2	Randomize the orientation of the second docking partner. (Only works with 2 partner docking).	Boolean
-spin	Spin a second docking partner around axes from center of mass of the first partner to the second partner.	Boolean
-dock_pert [T] [R] -dock_pert TRANSLATION_in_Angstrom ROTATION_in_degrees -dock_pert 3 8	Do a small perturbation with the second partner around the first partner.	RealVector
-uniform_trans [R] -uniform_trans 10	Uniform random repositioning of the second partner about the first partner within a sphere of the given radius.	Real

Packing flags

-norepack1	Do not repack the sidechains on the first docking partner. (Only works with 2 partner docking).	Boolean
-norepack2	Do not repack the sidechains on the second docking partner.	Boolean
-sc_min	Perform extra side chain minimization steps during packing steps.	Boolean

Full Protocol flags

Default mode of docking. No protocol flags necessary.

Low Resolution Protocol Flags

-low_res_protocol_only

Only run the low resolution part of the protocol (skips all high resolution steps and only outputs low resolution structure).

Boolean

High Resolution Protocol Flags

-docking_local_refine

Refine the docking position in high resolution only (skips all low resolution steps of the protocol). Uses small perturbations of the positions, no large moves.

Boolean

High Resolution Minimization Cycle Protocol Flags

-docking_local_refine	Refine the docking position in high resolution only (skips all low resolution steps of the protocol). Uses small perturbations of the positions, no large moves.	Boolean
-dock_min	Does a single round of minimization in high resolution, skipping the mcm protocol.	Boolean

Relevant common Rosetta Flags

-s [S] -s 1abc.pdb OR -silent [S] -silent 1abc.silent	Specify starting structure (in:file:s for PDB format, in:file:silent for silent file format).	String
-native [S] -natie 1abc.native.pdb	Specify the native structure for which to compare in RMSD calculations. If a native file is not passed in, all calculations are done using the starting structure as native.	String
-nstruct [I] -nstruct 100		Integer
-database [P] -database ~/minirosetta_database	The Rosetta database.	String
-use_input_sc	Use accepted rotamers from the input structure between Monte-Carlo with Minimization (MCM) cycles. Unlike the -unboundrot flag, not all rotamers from the input structure are added each time to the rotamer library, but only those accepted at the end of each round the remaining conformations are lost.	Boolean
-ex1/-ex1aro -ex2/-ex2aro -ex3 -ex4	Adding extra side-chain rotamers (highly recommended). The -ex1 and -ex2aro flags were used in our own tests, and therefore are recommended as default values. See <link to="" side="" chain="" documentation>=""> for more information	Boolean/Integer

Expert Flags

-use_new_protocol	Use a version of the high resolution docking that more closely matches published algorithms.	Boolean
-dock_mcm_trans_magnitude [T] -dock_mcm_trans_magnitude 0.1	The magnitude of the translational perturbation during mcm steps in docking.	Real
-dock_mcm_rot_magnitude [R] -dock_mcm_rot_magnitude 5.0	The magnitude of the rotational perturbation during mcm steps in docking.	Real
-docking_centroid_outer_cycles [C] -docking_centroid_outer_cycles 10	Number of cycles to use in outer loop of docking low resolution protocol.	Integer
-docking_centroid_inner_cycles [C] -docking_centroid_inner_cycles 50	Number of cycles to use in inner loop of docking low resolution protocol.	Integer

Tips

The docking run can take two forms, depending on one's confidence in the native structure. Sometimes biochemical and genetic information can be used to localize the binding site to a small region on one or both partners. In this case, one performs a perturbation run, exploring only a small region of space around the suspected binding site. For predictions where there is no biological information about the interface, one usually performs a global search, exploring all the conformational space of both partners.

Docking is most effective when used for local perturbations. If a bound structure is available, it is often worthwhile to perform a local refine on that structure to make sure an energy funnel is present in the native structure.

Global docking simulations give poor results when there are more than 450 residues in the complex.

The most commonly used options are -dock_pert 3 8, which will allow translations within 3 Angstroms and rotations within 8 degrees in low resolution mode and -docking_local_refine, which will only perform high resolution docking.