|Rosetta 3.2 Release Manual|
mini/test/integration/tests/fold_and_dockfor an example of fold-and/dock protocol and input files. Run without the -run:test_cycles for a real case prediction example. Fold-and-dock uses the topology broker framework and the actual excecutable is the minirosetta application,
Depending on the user the protocol can then move into the all-atom refinement stage by calling the relax code. The relax code is sensitive to the presense of symmetry and relaxes the protein while maintaining the overall symmetry of the system.
Limitations: The protocol nly works on symmetric structures. It will most likely not work for protein in excess of 120 residues unless aditional experimental data is available.
CLAIMER FoldandDockClaimer END_CLAIMER
The fasta file and fragments is most easily supplied through command line options but can also be specified through the broker input file (see broker documentation for example).
-run:protocol broker - Tells rosetta application to run the broker -broker:setup - The location of broker setup file -database -file:frag3 -file:frag9 -in:file:fasta -symmetry:symmetry_definition -symmetry:initialize_rigid_body_dofs - Setup the rigid body system according to the symmetry definition file. -run:reinitialize_mover_for_each_job - Since an oligomer is made from a monomer we need to start fresh with a monomer for each simulation. -out:file:silent_struct_type binary - Currently the only silent file type that is compatible with symmetry.
-fold_and_dock:rigid_body_cycles - Number of rigid bosy cycles during fold and dock fragment insertion -fold_and_dock:move_anchor_points - Move the anchor points that define symmetric coordinate system during symmetry fragment insertion. -fold_and_dock:set_anchor_at_closest_point - Set the anchor points that define symmetric coordinate system to the nearest point between two consecutive chains during fragment insertion. -fold_and_dock:rotate_anchor_to_x - Rotate the anchor residue to the x-axis before applying rigid body transformations. -fold_and_dock:trans_mag_smooth - Translation perturbation size for smooth refineme. -fold_and_dock:rot_mag_smooth - Rotational perturbation size for smooth refinement. -fold_and_dock:rb_rot_magnitude - Rotational perturbation size for rigid body pertubations. -fold_and_dock:rb_trans_magnitude Translational perturbation size rigid body pertubations. -fold_and_dock:rigid_body_cycles - Number of rigid bosy cycles during fold and dock fragment insertion. -fold_and_dock:rigid_body_frequency - The fraction of times rigid body cycles are applied during fragment assembly moves. -fold_and_dock:rigid_body_disable_mc - Dissallow moves to be accepted locally by Monte Carlo criteria within the rigid body mover. -fold_and_dock:slide_contact_frequency - The fraction of times subunits are slided together during fragment assembly moves.
-evaluation:rmsd_target - The reference pdb. It should be a oligomer with the same number of residues and sequence as the structure outputted by rosetta. -evaluation:rmsd_column - Name of the output column in the scorefile and silent output file. evaluation:symmetric_rmsd - Find the lowest rmds vs the native by considering all possible chain orderings. Necessary to get the right rms for systems with more than 2 subunits. May not be necessary if a local perturbation or dock_pert is performed, if the input has the matching chain order. The number of rms calculations grows exponentially with number of subunits, so for large systems it will be very slow.
Running fold-and-dock with chemical shift data follows the same procedure as regular abinitio. Just supply fold-and-dock with fragment libraries picked with chemical shift data.
For many systems it is not necessary to explicitly simulate all subunits in the symmetrical systems. for example in a dodecamer with cyclical symmetry a subunit only interacts with neighbor subunits to the left or right of it in the ring. With the make_symmdef_file_denovo you can add the -subsystem option to generate a smaller symmetry definition for a smaller system. With the make_symmdef_file script this can be controlled by finetuning the cutoff distance.
CPU Time: This is very dependent on the size of the protein. For most proteins it will be about 1-15 minutes per model. So the CPU time to generate a funneled energy landscape would vary between 150-10 000 CPU hours.
The following flags have been succesfull in repeating the result of the fold-and-dock benchmark in the original paper and is a good starting point.
-run:protocol broker -broker:setup -nstruct -out:file:scorefile -database -file:frag3 -file:frag9 -in:file:fasta -symmetry:symmetry_definition -out:file:silent -out:file:silent_struct_type binary -relax:fast -relax:jump_move -symmetry:initialize_rigid_body_dofs -fold_and_dock::rotate_anchor_to_x // May even be a required flag... -evaluation:rmsd_target -evaluation:rmsd_column -evaluation:symmetric_rmsd -rg_reweight 0.001 // Rewight the rg scoring term. For extended structures like coiled-coils this is crucial. For global structures perhaps not as beneficial. -rigid_body_cycles 1 // Works in conjuction with rigid_body_disable_mc -abinitio::recover_low_in_stages 0 // The lowest energy structure is not always selected after each stage. This prevents overoptimization of low-resolution energy but may not be optimal for all cases. -rigid_body_frequency 5 -rigid_body_disable_mc // Makes sure that the rigid body moves are accepted by the same Monte Carlo process as the fragment sampling. This prevents overoptimization of low-resolution energy but may not be optimal for all cases. -run:reinitialize_mover_for_each_job