The scientific component of docking protocol is the same as the original RosettaDock. The docking protocol is still based on the RosettaDock algorithms. RosettaDock works by simultaneous optimization of side-chain conformation and rigid body position of the two docking partners. The former is performed by a packing algorithm, and the latter is performed by a rigid-body Monte Carlo Minimization (MCM) strategy. For more, on understanding RosettaDock see RosettaDock tutorials: http://graylab.jhu.edu/~mdaily/tutorial/basics_main.html
We have one dock application ready at rosetta_source/src/apps/public/docking The name of the applications is docking_protocol. You can find the executable of this application in rosetta_source/bin/ after successfully compiling. With this application you can do all major rigid-body docking functions from Rosetta, including global docking, local perturbations, and high-resolution refinement of complex structures.
RosettaDock application's input file is a PDB file which holds two docking partners.The two independently movable protein units in Rosetta. For a complex of two polypeptide chains, a docking partner has the same meaning as a polypeptide chain. For three or more chains (e.g. in an antibody-antigen run), a docking partner contains multiple chains. Each partner is ended by a "TER" mark in the pdb file.
Rosetta 3.1 Release Manual
There are two kinds of output files generated during a docking run. One is pdb file, the other is energy fasc (fullatom scoring) file.
docking_protocol.linuxgccrelease @flags > docking,log&
Options used in RosettaDock.
-in:database Path to Rosetta databases. [PathVector]
-in:file:s Input file path.[FileVector]
-nstruct Number of output structures per use. [Interger]
-docking:dock_pert Initial perturbation: Do a small perturbation with partner two. Followed by DEGREES and ANGSTROMS. Standard values for a local
perturbation are 3D and 8A.[RealVector] For Example: -docking:dock_pert <degrees> <angstroms>
-docking:spin Initial perturbation: Spin a second docking partner around axes from center of mass of partner 1 to partner 2. [Boolean]
-docking:randomize1 Initial perturbation: Randomize the first docking partner. [Boolean]
-docking:randomize2 Initial perturbation: Randomize the second docking partner. [Boolean]
-docking:docking_local_refine Initial perturbation: skips initial perturbation and centroid mode search and goes direct to fullatom mode.[Boolean]
-ex1 -ex2_aro Standard side chain flags for using expanded rotamer libraries during packing for fullatom docking. [Boolean]
-docking:dock_ppk Fullatom mode: prepacking Pack all side chains of component proteins to lowest energy conformation. [Boolean]
-docking:dock_min Fullatom mode: energy minimization. Does a rigid-body energy minimization instead of MCM. [Boolean]
-out:file:fullatom Enable full-atom output of pdb.[Boolean]
-out:file:o Name of the output score file.[String]
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, in press, DOI, http://dx.doi.org/10.1016/j.jmb.2007.07.05 [update!]
total_score: Final Score.
rms: Rmsd of the decoy to the native.
cen_rms: RMSD of the decoy following centroid mode, to the native.
dslf_ca_dih: ca dihedral score in current disulfide
dslf_cs_ang: csangles score in current disulfide
dslf_ss_dih: dihedral score in current disulfide
dslf_ss_dst: distance score in current disulfide
fa_atr: lennard-jones attractive.
fa_dun: internal energy of sidechain rotamers as derived from Dunbrack's statistics.
fa_rep: lennard-jones repulsive.
fa_sol: lazaridis-karplus solvation energy.
hbond_bb_sc: sidechain-backbone hydrogen bond energy
hbond_lr_bb: backbone-backbone hbonds distant in primary sequence
hbond_sc: sidechain-sidechain hydrogen bond energy
hbond_sr_bb: backbone-backbone hbonds close in primary sequence
interchain_env: interface environmental effects
interchain_pair: pairwise interactions
interchain_vdw: Van der Waals
ref: reference energy for each amino acid
st_rmsd: RMSD of the decoy following the initial perturbation, to the native
description: input pdb tags
Generated on Tue Apr 20 07:50:05 2010 for Rosetta Projects by
© Copyright Rosetta Commons Member Institutions. For more information, see http://www.rosettacommons.org.