Table 2.

A summary of the main features of different approaches to TBM of protein-protein complexes.

Approach	Template libraries required	Monomer template search method	Complex template search method	Complex structure construction	Advantages (limitations)
Dimeric threading (Fig. 2a without blue parts)	Dimer template library	None	Dimeric threading	Dimer structure copied from template proteins	Alignment considering interfacial interactions dimer library is limited)
Extended dimeric threading (Fig. 2a with blue parts)	Dimer template library plus separate monomer template library	Monomeric threading	Dimeric threading	Superposition of monomer templates onto dimeric template	Improved models for individual subunits
Monomer threading and oligomer mapping (Fig. 2b)	Combined library of monomer and oligomer structures	Monomeric threading	Framework mapped from monomeric threading	Superposition of monomer templates onto oligomer subunits	A single template library covering different binding modes
Template-based docking (Fig. 2c)	Library of complexes or interfaces	Typically starts from monomer structures/models	Monomer to complex structural alignments	Superposition of monomer models onto the complex interface templates	Potential to detect non-homologous templates
Full-length complex structure simulation	None	None	None	Reassemble template structures by Monte Carlo simulations	Construction of full-length model and potential of structure refinement