Table 1: Comparison of the lowest lRMSDs obtained by BH to those obtained by other methods on the protein dimers studied here. MBH refers to monotonic BH. lRMSDs reported by BH, MBH, and the work in [56] in columns 5–7 are over backbone atoms, whereas those reported by the work in [36, 84] in columns 8-9 are over alpha carbons of the backbone chain.

Number PDB ID Length Fold BH (Å) MBH (Å) [56] (Å) [36] (Å) [84] (Å)

1 1dtdB 61 6.9 6.6 7.5 6.5 5.7
2 1isuA 62 6.3 6.5 6.5 6.5 6.9
3 1c8cA 64 6.5 5.7 7.2 3.7 5.0
4 1sap 66 6.5 6.0 7.36 4.6 6.6
5 1hz6A 67 5.7 6.0 6.6 3.8 3.4
6 1wapA 68 7.4 8.1 7.3 8.0 7.7
7 1fwp 69 6.3 6.7 7.1 8.1 7.3
8 1ail 70 3.2 4.2 4.0 5.4 6.0
9 1aoy 78 5.7 6.1 5.8 5.7 5.7
10 1cc5 83 5.8 5.6 5.8 6.5 6.2
11 2ezk 93 4.3 5.8 6.0 5.5 6.6
12 1hhp 99 10.4 10.5 11.0 NA NA
13 2hg6 106 8.8 9.3 9.7 NA NA
14 3gwl 106 4.9 4.9 6.3 NA NA
15 2h5nD 123 7.5 7.8 8.6 NA NA