Table IV. Results for the construction of protein assemblies starting from alternative conformations of the unbound forms.

PDB structure	Number of chains	Number of residues	Target set	Energy unit	RMSD (Å)
1eer	3	620	1gia, 1tbgA, 1tbgE	−75.58	5.56
1eer	3	620	1gia, 1gg2A, 1tbgA, 1tbgE	−122.19	3.23
1gp2	3	764	1buyA, 1ernA x2	−279.38	3.57
1gp2	3	764	1buyA, 1ernA x2, 1cn4C, 1ebaA x2	−376.18	2.50

Predicted PDB structures are given with their PDB I.D., number of chains, and number of residues. Target set includes unbound forms and their alternative conformations found in the PDB. If an unbound structure is used twice, it is denoted by “x2.” Different target sets are used: (i) a target set of unbound forms and (ii) a target set of unbound forms and their alternative structures. Their best energy predictions are compared with respect to energy scores and RMSD values. RMSD was calculated for all backbone atoms, and the energy value of an assembly is the summation of energy values calculated for the addition of each protein.