DESCRIPTION:

Evaluate an interface using Mouse. We also find that Mouse performs better when given a bias towards large interfaces, so we built that in using the add_interface_size_bonus and interfaces_residues options.

There is also a score type mouse that wraps this simple metric to be easier to use with a score function.

USAGE:

<MouseTotalEnergy custom_type=(string) surface_only=(bool,"true") add_interface_size_bonus=(bool,"false") interfaces_residues=(string) residue_selector=(string) name=(string)/>

OPTIONS:

"MouseTotalEnergy" tag:

• custom_type (string): Allows multiple configured SimpleMetrics of a single type to be called in a single RunSimpleMetrics and SimpleMetricFeatures. The custom_type name will be added to the data tag in the scorefile or features database.

• surface_only (bool,"true"): Only score residues at each chain's surface (including interfaces). This is highly recommended because it is what MOUSE was trained to do.

• add_interface_size_bonus (bool,"false"): Subtract the number of interface residues from the final score (-1 REU bonus per interface residue). This is highly recommended because MOUSE does not inherently bias itself towards large interfaces but we see a hugh advantage when adding this bonus. Requires the interfaces_residues option to be supplied.

• interfaces_residues (string): This needs to be the name of a residue selector. These are the residues that are given a bonus by the add_interface_size_bonus option. This is ENTIRELY orthogonal to the residue_selector option. You still need to pass add_interface_size_bonus="true" when you use this feature.

• residue_selector (string): If a residue selector is present, we calculate the total energy of only these residues. If surface_only=true, we will only use a subset of the residues provided by the residue selector.

• name (string): The name given to this instance.

## Example in action:

<ROSETTASCRIPTS>
<SCOREFXNS>
<ScoreFunction name="highres" weights="ref2015.wts"/>
<ScoreFunction name="lowres" weights="score3.wts"/>
</SCOREFXNS>

<RESIDUE_SELECTORS>
<Chain name="chainA" chains="A"/>
<Chain name="chainB" chains="B"/>
<InterfaceByVector name="interface" grp1_selector="chainA" grp2_selector="chainB"/>
</RESIDUE_SELECTORS>

<!-- Let's just say this is one-sided design to give an example -->
<OperateOnResidueSubset name="one_sided_design" selector="chainA" >
<RestrictToRepackingRLT/>
</OperateOnResidueSubset>

<MOVERS>
<MouseSpyDockingProtocol name="mouse_spy" docking_score_low="lowres" spy_count="15"/>
<MouseFinalizeMover name="mouse_finalize"/>

<RunSimpleMetrics name="run_sm" prefix="after_docking_">
<MousePerResidueEnergy custom_type="per_res" />
<MouseTotalEnergy custom_type="total" />
</RunSimpleMetrics>
</MOVERS>

<PROTOCOLS>
<!-- Pose is converted to centroid mode. Original sidechains are stored in the pose. -->
<!-- No need for the silly SaveAndRetrieveSidechains mover. -->

<!-- Drop-in replacement for DockingProtocol -->

<!-- Make sure to run all Mouse-related protocols before the finalize mover, including simple metrics -->
</ROSETTASCRIPTS>