Table 1.

List of methods for template-based protein complex structure prediction.

Methods [Ref.]a	Method typeb	Interaction predictionc	Structure predictiond	Large- scale appe	Web site
Interactome3D [65•]	DT	−	refined	[65•]	http://interactome3d.irbbarcelona.org/
InterPreTS [44,48]	DT	+	crude	[30]	http://www.russelllab.org/cgi-bin/tools/interprets.pl
ABCLM [30]	DT & TBD	+	unrefined	[30]
SPRING [21••]	MOM	−	crude	[21••]	http://zhanglab.ccmb.med.umich.edu/spring/
COTH [18•]	DT	−	crude	[18•]	http://zhanglab.ccmb.med.umich.edu/COTH/
TACOS	DT & FSS	−	refined	-	http://zhanglab.ccmb.med.umich.edu/TACOS/
Multiprospector [24]	DT	+	crude	[69]
M-TASSER [28]	DT & FSS	−	refined	-
PrePPI [20••]	TBD	+	crude	[20••]	http://bhapp.c2b2.columbia.edu/PrePPI/
Coev2Net [47•]	DT	+	-	[47•]	http://groups.csail.mit.edu/cb/coev2net/
Struct2Net [26,50]	DT	+	crude	[26]	http://groups.csail.mit.edu/cb/struct2net/webserver/
iWrap [27]	DT	+	crude	[27]	http://groups.csail.mit.edu/cb/iwrap/
PRISM [23,46]	TBD	+	unrefined	[23,70]	http://prism.ccbb.ku.edu.tr/
SKV [19•]	TBD	−	unrefined	-
HOMBACOP [25]	DT	+	refined	[72•]
KA [71]	DT & TBD	+	crude	[72•]
HOMCOS [45,49]	DT	−	refined	[49]	http://strcomp.protein.osaka-u.ac.jp/homcos/
THSWP [38]	DT	+	crude	[38]

^aThe methods without an explicit name are represented by an acronym formed from the authors’ initials.

^bType of methods, categorized into dimeric threading (DT), monomer threading and oligomer mapping (MOM), template-based docking (TBD), and full-length complex structure simulation (FSS), following the categorizations in Figure 2 and Table 2.

^c“+”means that the method provides information about the existence of protein-protein interaction, whereby “-” means that the method does not conduct interaction prediction.

^d“crude” indicates that the method only provides a raw alignment of query and template proteins with gaps/insertions; “unrefined” means that the monomer chains are continuous but no further refinement was carried out; “refined” refers to the methods with some type of structure optimizations.

^eThe literature that applied the developed methods to a large-score protein complex structure modeling.