Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules

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