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This set of applications and tools is specifically designed to work with antibodies. Before using these applications, you may want to check the General Antibody Options and Tips page.

Table of Contents

Antibody Modeling

Antibody Docking

Antibody Utilities

  • CDR Cluster Identification: An application that matches each CDR of an antibody to North/Dunbrack CDR clusters based on the lowest dihedral distance to each cluster center.

Using Rosetta Scripts for Antibody Modeling and Design

You can use the collection of TaskOperations and Movers to write your own Antibody modeling and design protocol. For example, this set of TaskOps would design a set of heavy chain CDRs and neighboring framework residues with North/Dunbrack CDR Cluster profiles as well as whole CDR sequence sampling, while leaving H3 to design using all residues.

<ROSETTASCRIPTS>
	<SCOREFXNS>
	</SCOREFXNS>
	<TASKOPERATIONS>
	  <RestrictToCDRsAndNeighbors name=to_cdrs/>
	  <DisableCDRsOperations name=disable_L cdrs=L1,L2,L3 />
	  <AddCDRProfilesOperation name=profiles cdrs=H1,H2 />
	  <AddCDRProfileSetsOperation mame=sets cdrs=H1,H2 />
	  <DisableAntibodyRegionOperation name=disable_antigen region=antigen_region/>
	</TASKOPERATIONS>
	<FILTERS>
	</FILTERS>
	<MOVERS>
		<PackRotamersMover name=packrot scorefxn=sf task_operations=to_cdrs,disable_L,profiles,sets,disable_antigen/>
	</MOVERS>
	<APPLY_TO_POSE>
	</APPLY_TO_POSE>
	<PROTOCOLS>
		<Add mover_name=packrot />
	</PROTOCOLS>
	<OUTPUT />
</ROSETTASCRIPTS>

Ab TaskOperations

Ab Movers

Ab Structure Editing

See Also