Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

Table 2 Distance from the native structure

				local		avg (min) lowest lRMSD to native in Å
	PDB id	len	fold	search len	PLOW	Naive Sampling	FeLTr	FeLTr*	Sosnick	Baker
1	1DTDB	61	αβ	160	7.0(6.3)	6.9(6.0)	7.7(6.8)	7.5(7.0)	6.5	5.7
2	1ISUA	62	αβ	173	6.1(6.0)	6.7(6.6)	6.6(6.3)	6.5(5.7)	6.5	6.9
3	1C8CA	64	αβ	199	7.3(6.9)	7.2(6.8)	6.8(6.0)	7.2(5.8)	3.7	5.0
4	1SAP	66	αβ	211	6.7(6.2)	7.0(6.3)	7.1(6.5)	7.3(6.8)	4.6	6.6
5	1HZ6A	67	αβ	182	6.3(6.1)	5.8(5.6)	6.7(6.6)	6.6(6.1)	3.8	3.4
6	1WAPA	68	β	199	7.4(6.9)	7.8(7.6)	8.1(7.3)	7.3(6.5)	8.0	7.7
7	1FWP	69	αβ	210	6.3(5.2)	6.5(6.0)	7.3(6.4)	7.1(6.8)	8.1	7.3
8	1AIL	70	α	237	2.8(2.0)	4.1(3.8)	4.8(4.5)	4.0(3.4)	5.4	6.0
9	1AOY	78	αβ	258	5.6(5.3)	6.3(5.8)	5.2(4.6)	5.8(5.2)	5.7	5.7
10	1CC5	83	α	274	5.7(5.4)	5.5(4.7)	6.2(5.6)	5.8(4.9)	6.5	6.2
11	2EZK	93	α	293	4.7(4.3)	4.9(4.5)	6.5(6.0)	6.0(4.7)	5.5	6.6
12	1HHP	99	αβ	306	10.2(9.7)	10.8(10.3)	11.2(10.0)	11.0(9.7)	NA	NA
13	2HG6	106	αβ	376	8.9(8.1)	9.7(9.2)	10.0(9.6)	9.7(9.0)	NA	NA
14	3GWL	106	α	375	4.3(3.7)	5.7(5.5)	6.6(5.7)	6.3(4.4)	NA	NA
15	2H5ND	123	α	482	7.3(6.8)	8.3(8.0)	9.0(8.5)	8.6(7.8)	NA	NA

The lowest lRMSD to the native structure achieved is shown for our new PLOW framework, the naive sampling approach, and our previously developed FeLTr framework as well as published results from the Sosnick [18] and Baker [47] research groups. The lRMSDs shown are the average over five runs, with the minimum of the five runs shown in parentheses. Column 5 shows the average number of iterations each PLOW greedy search ran for. FeLTr* represents the FeLTr framework using the value from column 5 as its MMC search length.

ISSN: 1477-5956