Table 3. Comparison of the structural properties between OPEP and GROMACS structures for selected stable structures.

			β-Sheet Contenent (based on the dssp program)(b)				% Parallel - Antiparallel(c)				% Res Align (% 100 Align - % Shift by 1 Res - % Shift by 2 Res…)(d)
			GROMACS - GR		OPEP - OP		GROMACS - GR		OPEP - OP		GROMACS - GR		OPEP - OP
	Configuration Type(a)	Structure	First Cluster	Final Structure	CG	Min	First Cluster	Final Structure	CG	Min	First Cluster	Final Structure	CG	Min
Trimers	3	03_1 - A	38%	19%	71% (100%)	67%	50 - 50	50 - 0	50 - 50	50 - 50	50 - 50	50 - 50	50 - 50	50 - 50
	3	03_1 - B	38%	24%	19% (27%)	67%	0 - 50	50 - 50	50 - 50	50 - 50	50 - 50	50 - 0 - 50	50 - 50	50 - 50
	3	03_1 - C	57%	62%	62% (87%)	67%	50 - 50	50 - 50	50 - 50	50 - 50	50 - 50	50 - 50	50 - 50	50 - 50
	3	03_1 - D	48%	57%	52% (73%)	67%	0 - 50	0 - 50	0 - 50	0 - 100	50 - 50	50 - 50	50 - 50	50 - 50
	3	03_1 - E	48%	52%	57% (80%)	53%	50 - 50	0 - 50	0 - 50	0 - 100	50 - 0 - 50	50 - 0 - 50	0 - 50 - 50	0 - 50 - 50
12-mers	12	12_1 - A	49%	35%	64% (90%)	60%	60 - 20	40 - 10	36 - 64	36 - 64	80 - 20	50 - 50	64 - 18 - 18	64 - 18 - 18
	6 4 1	12_1 - B	14%	14%	45% (63%)	44%	13 - 25	20 - 40	22 - 22	33 - 33	35 - 25 - 37	0 - 40 - 60	33 - 56 - 11	33 - 56 - 11
	8 4	12_1 - C	35%	29%	49% (68%)	42%	10 - 20	40 - 20	60 - 40	40 - 30	40 - 40 - 20	50 - 20 - 30	60 - 20 - 20	60 - 20 - 20
	7 5	12_1 - D	33%	24%	54% (75%)	55%	11 - 22	0 - 30	40 - 60	10 - 60	45 - 44 - 11	50 - 50	50 - 50	50 - 50
	7 5	12_1 - E	56%	51%	46%	51%	60 - 40	50 - 20	60 - 40	60 - 40	60 - 30 - 10	50 - 50	60 - 30 - 10	50 - 40 -10
20-mers	11 7 1 1	20_p - A1	43%	38%	38% (53%)	37%	44 - 6	56 - 13	76 - 24	44 - 25	56 - 31 - 13	63 - 19 - 18	34 - 33 - 33	44 - 37 - 19
		20_p - A2	31%	34%	38% (53%)	37%	33 - 0	50 - 0	76 - 24	44 - 25	40 - 40 - 20	63 - 31 - 6	34 - 33 - 33	44 - 37 - 19
	11 7 1 1	20_p - B1	52%	49%	36% (50%)	66%	69 - 19	59 - 12	71 -24	75 - 25	31 - 44 - 25	35 - 47 -18	33 - 39 - 28	31 - 44 - 25
		20_p - B2	47%	38%	36% (50%)	66%	40 - 13	38 - 13	71 -24	75 - 25	34 - 53 - 13	31 - 56 - 13	33 - 39 - 28	31 - 44 - 25
	11 7 1 1	20_p - C1	39%	35%	44% (44%)	59%	44 - 19	47 - 20	72 - 22	69 - 25	31 - 50 - 19	54 - 33 -13	33 - 39 - 28	31 - 44 - 25
		20_p - C2	59%	36%	44% (44%)	59%	69 - 25	69 - 8	72 - 22	69 - 25	27 - 47 - 26	46 - 54	33 - 39 - 28	31 - 44 - 25
	12 7 1	20_p - D1	44%	46%	44% (62%)	64%	24 - 35	24 - 35	35 - 47	41 -47	59 - 35 - 6	65 - 33 -6	59 - 35 - 6	59 - 35 - 6
		20_p - D2	27%	27%	44% (62%)	64%	29 - 24	22 - 22	35 - 47	41 - 47	63 - 31 - 6	61 - 33 -6	59 - 35 - 6	59 - 35 - 6
	9 6 5	20_2 - A	44%	44%	34% (47%)	28%	69 - 13	61 - 11	72 - 22	73 - 13	31 - 44 -25	39 - 39 - 22	56 - 39 - 5	20 - 53 - 27
	8 7 5	20_2 - B	45%	39%	39% (55%)	71%	41 - 41	17 - 22	71 - 18	41 - 59	41 - 18 - 41	56 - 28 - 16	35 - 53 - 12	41 - 24 - 35
	7 7 6	20_2 - C	36%	37%	52% (73%)	65%	44 - 17	41 - 35	76 - 24	59 - 41	50 - 39 - 11	35 - 47 - 18	30 - 41 - 29	41 - 47 - 12
	8 8 4	20_2 - E	32%	33%	51% (72%)	63%	28 - 11	42 - 16	59 - 41	50 - 39	44 - 39 - 17	42 - 37 - 21	54 - 23 -23	39 - 33 - 28
	10 8 2	20_2 - N	41%	39%	42% (59%)	57%	39 - 22	41 - 24	31 - 56	31 - 56	44 - 28 - 28	29 - 47 - 24	44 - 25 -31	44 - 25 - 31

“First Cluster” means the most representative structure of the GROMACS simulations. “Final structure” is the final conformation obtained at the end of the GROMACS simulations. “CG” is the structure extracted at the end of the OPEP simulations before the reconstruction of the side chains. “Min” indicates the structure resulting from the reconstruction of the side chains after a minimization step.

^(a)The configuration type (as described in the OPEP Analysis and Structure Selection section).

^(b)The average amount (percentage) of residues in a β conformation. For OPEP, the percentage in brackets has been calculated without taking the Glycines into account.

^(c)The average amount (percentage) of parallel and anti-parallel strands in a structure. The sum of parallel and antiparallel strands in a structure does not always total 100% if the structure sees strands in an undefined orientation, i.e. attached by only one hydrogen bond.

^(d)The average amount of strands in-register and out-of-register (by one residue).