Table 1.

Naming conventions of methods described in this work.

Name	Description
C-PPA	A multiple-chain threading algorithm with scoring function including profile-profile and secondary structure matches. It is an extension of the PPA algorithm for monomer threading (Wu et al., 2007).
C-MUSTER	A multiple-chain threading algorithms with scoring function including similar terms to C-PPA, plus multiple structure-based terms derived for torsion-angle and structural profile matches. It is an extension of the MUSTER algorithm for monomer threading (Wu and Zhang, 2008).
COTH threading	A multiple-chain threading algorithm with scoring function including similar terms to C-MUSTER, plus the binding site match. The binding sites for targets are predicted by BSpred.
COTH	Models are generated by combining the tertiary templates from MUSTER with the quaternary templates from COTH-threading through structure superposition.
COTH-exp	Models are generated by superimposing the experimental unbound monomer structures onto the templates from COTH-threading.
COTH-model	Models are generated by superimposing the full-length monomer models onto the templates from COTH-threading. The monomer models were predicted by MUSTER with loops filled by MODELLER.
ZDOCK-exp	Models are generated by ZDOCK which docks the experimental unbound monomer structures followed by RDOCK refinement.
ZDOCK-model	Models are generated by ZDOCK which docks the full-length monomer models predicted by MUSTER and MODELLER, followed by RDOCK refinement.