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.
Antibody Design Strategy Analysis: A PyRosetta-based tool to analyze and/or compare antibody design strategies.
CDR Cluster Constrained Relax: An application to relax CDRs using circular harmonic constraints based on identified CDR clusters.
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>