Table 1. Overview of Available Protocols in Rosetta for Antibody and Antigen Modeling and Design.

name	implementation	weblink	ref
Antibody Structure Prediction
RosettaAntibody	Application	https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol	Weitzner et al.4
			Weitzner et al.25
			Sivasubramian et al.26
AbPredict	XML	http://abpredict.weizmann.ac.il	Norn et al.27
		https://www.rosettacommons.org/demos/latest/tutorials/AbPredict/AbPredict
RosettaCM	XML	https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/RosettaCM	Song et al.28
Antibody–Antigen Docking
RosettaDock	XML	https://www.rosettacommons.org/docs/latest/application_documentation/docking/docking-protocol	Gray et al.29
		https://rosie.rosettacommons.org/docking/	Chaudhury et al.30
			Chaudhury et al.31
			Marze et al.32
SnugDock	Application	https://www.rosettacommons.org/docs/latest/application_documentation/antibody/snugdock	Weitzner et al.4
			Sirkar et al.33
Antibody Design
RosettaAntibodyDesign	Application	https://www.rosettacommons.org/docs/latest/application_documentation/antibody/RosettaAntibodyDesign	Adolf-Bryfogle et al.34
AbDesign	XML		Lapidoth et al.35
RECON	XML	https://www.rosettacommons.org/docs/latest/application_documentation/RECON-multistate-design	Sevy et al.5
			Sevy et al.6
MSD with negative design states	XML	https://www.rosettacommons.org/demos/latest/protocol_capture/multistate_apl/README	Leaver-Fay et al.36
Antigen Design
side chain and backbone grafting	XML	https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/MotifGraftMover	Azoitei et al.37
			Correia et al.38
			Silva et al.39
FunFolDes	XML	https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/composite_protocols/fold_from_loops/FunFolDes	Bonet et al.40
			Correia et al.11
Scaffold Design
RosettaRemodel	Application	https://www.rosettacommons.org/docs/latest/application_documentation/design/rosettaremodel	Huang et al.41
SEWING	XML	https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/composite_protocols/sewing/SEWING	Jacobs et al.42
			Guffy et al.43
PROSS	Webserver	https://pross.weizmann.ac.il/step/pross-terms/	Goldenzweig et al.44
Working with Glycans
GlycanTreeModeler	XML	https://www.rosettacommons.org/docs/latest/application_documentation/carbohydrates/WorkingWithGlycans	Adolf-Bryfogle et al. (publication in preparation)
	PyRosetta		Labonte et al.45