Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter

Table 1 local search.

	Native PDB id	Size	fold	% α	% β	Lowest Energy (kcal/mol)				Lowest lRMSD (Å)
						T = 0	T ₀	T ₁	T ₂	T = 0	T ₀	T ₁	T ₂
1	1dtdB	61	α/β	15	46	-128.2	-132.1	-131.6	-127.9	6.9	6.6	6.9	7.0
2	1isuA	62	α/β	15	19	-127.8	-130.3	-130.7	-130.2	6.3	6.0	6.4	6.0
3	1c8cA	64	α/β	22	48	-133.5	-134.8	-130.8	-129.6	6.5	6.6	7.4	7.3
4	1sap	66	α/β	30	44	-132.8	-132.3	-133.6	-127.3	6.5	6.0	6.8	6.9
5	1hz6A	67	α/β	31	42	-143.5	-144.7	-142.1	-138.9	5.7	5.9	6.0	6.0
6	1wapA	68	β	0	62	-118.4	-127.2	-133.9	-127.9	7.4	7.6	7.4	7.5
7	1fwp	69	α/β	30	26	-152.8	-152.0	-143.5	-143.2	6.3	6.7	6.5	6.1
8	1ail	70	α	84	0	-170.6	-171.0	-167.3	-168.4	3.2	3.2	3.4	3.3
9	1aoy	78	α/β	41	10	-183.9	-181.2	-180.8	-184.1	5.7	6.4	6.0	6.4
10	1cc5	83	α	47	4	-170.9	-171.5	-179.1	-173.8	5.8	5.7	5.8	5.8
11	2ezk	93	α	68	0	-217.3	-218.6	-224.4	-216.0	4.3	4.6	4.2	4.4
12	1hhp	99	β	7	48	-168.7	-175.4	-179.0	-175.9	10.4	10.4	10.0	10.5
13	2hg6	106	α/β	34	21	-233.6	-236.8	-239.5	-235.1	8.8	9.0	8.8	9.2
14	3gwl	106	α	70	0	-264.6	-270.4	-273.9	-267.3	4.9	4.9	4.4	5.2
15	2h5nD	123	α	71	2	-307.8	-313.0	-316.5	-313.2	7.5	7.9	7.4	8.1

Columns 2-4 show the native PDB id, size and fold topology for each of the 15 target protein systems. Columns 5 and 6 break the fold topology down as the percentage of amino acids which are part of ↵-helices and (3-sheets. Columns 7-10 report the minimum energy achieved for each temperature T of the minimization component of the BH framework. Columns 11-14 then report the corresponding lowest lRMSD to the native structure achieved for each T .

ISSN: 1477-5956