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>

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

   <MOVERS>
     <MouseSetupMover name="mouse_setup" jump_for_interface="1" task_operations="one_sided_design" />
     <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" />
       <MouseTotalEnergy custom_type="total_with_interface_bias" interface_residues="interface" add_interface_size_bonus="true"/>
     </RunSimpleMetrics>
   </MOVERS>

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

     <!-- Drop-in replacement for DockingProtocol -->
     <Add mover="mouse_spy"/>

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

     <!-- Delete Mouse's meta-data, convert back to full atom mode, restore original sidechains -->
     <Add mover="mouse_finalize"/>

     <!-- Since the sidechains are restored, the only difference between current pose and the original pose is the jump (docking) -->
   </PROTOCOLS>

   <!-- Of course, do some packing/design before evaluating this pose in high res -->
   <OUTPUT scorefxn="highres"/>

</ROSETTASCRIPTS>

See Also