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] |
The methods without an explicit name are represented by an acronym formed from the authors’ initials.
Type 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.
“+”means that the method provides information about the existence of protein-protein interaction, whereby “-” means that the method does not conduct interaction prediction.
“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.
The literature that applied the developed methods to a large-score protein complex structure modeling.