Table 2.

Structure-based protein domain identification methods.

Category	Method	Description	Year	URL	Reference
Structure-based	DomainParser	Use flow network represent protein structure, and identify domain based on maximum-flow/minimum-cut theorem.	2000	http://compbio.ornl.gov/structure/domainparser/	[49]
	PDP	Identify the dividing site that makes the contact density of the two parts lower than a threshold as the domain boundary.	2003	http://123d.ncifcrf.gov/	[50]
	DIAL	Identify the domain by clustering substructures on the basis of their spatial distances.	2005	http://www.ncbs.res.in/~faculty/mini/DIAL/home.html	[48]
	CATHEDRAL	Identifiy the domain by comparing target structure with structure templates in CATH.	2007	http://cathwww.biochem.ucl.ac.uk/cgi-bin/cath/CathedralServer.pl	[46]
	DDOMAIN	Identify the dividing site that makes the distance between the two parts exceed the threshold as the domain boundary.	2007	http://sparks.informatics.iupui.edu	[51]
	DHcL	Identify the domain by calculating the van der Waals model of protein.	2008	http://sitron.bccs.uib.no/dhcl/	[52]
	Sword	Assign structural domains through the hierarchical merging of protein units. SWORD provides different domain assignments using different merge schemes.	2017	www.dsimb.inserm.fr/sword/	[53]
Predcitedstructure-based	SnapDRAGON	DRAGON generates 100 models, and then structure-based domain assignment is used to parse the models into domains. Finally, a result is derived from the consistency of the predicted boundaries.	2002		[55]
	RosettaDOM	RosettaDOM is a hybrid method that uses homology-based methods to predict domain boundaries when homologous templates can be found. When lacking templates, Rosetta is used to generate models, and final domain boundary predictions are derived from the models.	2005		[54]
	OPUS-Dom	Generate a large ensemble of folded structure decoys by VECFOLD, and predicted domain boundaries are derived from the consistency of the domain boundary in the set of 3D models.	2009		[56]