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Hotspot-based sidechain placement. This is the main workhorse of the hot-spot centric method for protein-binder design. A paper describing the method and a benchmark will be published soon. The "stub" (hot-spot residue) is chosen at random from the provided stub set. To minimize towards the stub (during placement), the user can define a series of movers (StubMinimize tag) that can be combined with a weight. The weight determines the strength of the backbone stub constraints that will influence the mover it is paired with. Finally, a series of user-defined design movers (DesignMovers tag) are made and the result is filtered according to final_filter.
For complicated systems, there are a few limitations in PlaceStub that you should be aware of:
There are two main ways to use PlaceStub:
<PlaceStub name="(&string)" place_scaffold="(0 &bool)" triage_positions="(1 &bool)" chain_to_design="(2 &integer)" score_threshold="(0.0 &Real)" allowed_host_res="(&string)" stubfile="(&string)" minimize_rb="(0 &bool)" after_placement_filter="(true_filter &string)" final_filter="(true_filter &string)" max_cb_dist="(4.0 &Real)" hurry="(1 &bool)" add_constraints="(1 &bool)" stub_energy_threshold="(1.0 &Real)" leave_coord_csts="(0 &bool)" post_placement_sdev="(1.0 &Real)">
<StubMinimize>
<Add mover_name="(&string)" bb_cst_weight="(10, &Real)"/>
</StubMinimize>
<DesignMovers>
<Add mover_name="(&string)" use_constraints="(1 &bool)" coord_cst_std="(0.5 &Real)"/>
</DesignMovers>
<NotifyMovers>
<Add mover_name="(&string)"/>
</NotifyMovers>
</PlaceStub>
The available tracers are:
From-source-generated documentation below:
Autogenerated Tag Syntax Documentation:
The Hotspot-based sidechain placement. This is the main workhorse of the hot-spot centric method for protein-binder design.
<PlaceStub name="(&string;)" residue_numbers="(&string;)"
residue_numbers_setter="(&string;)"
chain_to_design="(2 &positive_integer;)" score_threshold="(0.0 ℜ)"
hurry="(false &bool;)" triage_positions="(true &bool;)"
stub_energy_threshold="(1.0 ℜ)" stubfile="(&string;)"
minimize_rb="(false &bool;)"
after_placement_filter="(true_filter &string;)"
final_filter="(true_filter &string;)" add_constraints="(true &bool;)"
max_cb_dist="(4.0 ℜ)" leave_coord_csts="(false &bool;)"
post_placement_sdev="(1.0 ℜ)" place_scaffold="(false &bool;)"
task_operations="(&task_operation_comma_separated_list;)"
packer_palette="(&named_packer_palette;)"
allowed_host_res="(&resnum_list_with_ranges;)"
reference_name="(&string;)" >
<StubMinimize >
<Add mover_name="(&string;)" bb_cst_weight="(10.0 ℜ)" />
</StubMinimize>
<DesignMovers >
<Add mover_name="(&string;)" use_constraints="(true &bool;)"
coord_cst_std="(0.5 ℜ)" />
</DesignMovers>
<NotifyMovers >
<Add mover_name="(&string;)" />
</NotifyMovers>
</PlaceStub>
Subtag StubMinimize: Defines Movers used to minimize w/r/t stub placement
Subtag Add:
Subtag DesignMovers: Defines Movers used to do design after stub placement
Subtag Add:
Subtag NotifyMovers: Defines Movers (named elsewhere in XML) that must be aware of the protected stub locations so they are not lost
Subtag Add:
Submovers: Submovers are used to determine what moves are used following stub placement. For example, once a stub has been selected, a StubMinimize mover can try to optimize the current pose towards that stub. A DesignMover can be used to design the pose around that stub. Using DesignMover submovers within PlaceStub (instead of RepackMinimize movers outside PlaceStub) allows one to have a "memory" of which stub has been used. In this way, a DesignMover can fail a filter without causing the trajectory to completely reset. Instead, the outer PlaceStub mover will select another stub, and the trajectory will continue. There are two types of sub movers that can be called within the mover.
StubMinimize Without defining this submover, the protocol will simply perform a rigid body minimization as well as sc minimization of previous placed stubs in order to minimize towards the stub. Otherwise, a series of previously defined movers can be added, such as backrub, that will be applied for the stub minimization step. Before and after the list of stub minimize movers, there will be a rigid body minimization and a sc minimization of previously placed stubs. The bb_cst_weight determines how strong the constraints are that are derived from the stubs.
Valid/sensible StubMinimize movers are:
DesignMovers Design movers are typically used once the stubs are placed to fill up the remaining interface, since placestub does not actually introduce any further design other than stub placement.
Valid/sensible DesignMovers are:
NotifyMovers Movers placed in this section will be notified not to repack the PlaceStub-placed residues. This is not necessary if placement movers are used in a nested (recursive) fashion, as the placement movers automatically notify movers nested in them of the hot-spot residues. Essentially, you want to make the downstream movers (you list under this section) aware about the placement decisions in this upstream mover. These movers will not be run at in this placestub, but will be subsequently aware of placed residues for subsequent use. Useful for running design moves after placestub is done, e.g., in loops. Put task awareness only in the deepest placestub mover (if PlaceStub is nested), where the final decisions about which residues harbour hot-spot residues is made.