Table S1.

Execution times (in minutes) for enzyme–inhibitor docking set (1BOYV excluded)

Complex	FMFT 1 core	PIPER 1 core	FMFT 16 cores	PIPER 16 cores
1acb	12.20	157.38	2.05	14.42
1avx	12.79	164.77	2.09	14.70
1ay7	10.99	74.50	1.62	5.99
1bvn	16.33	173.40	2.67	21.68
1cgi	12.81	121.18	2.01	10.47
1clv	16.51	119.63	3.50	10.00
1d6r	13.17	156.53	2.99	12.87
1dfj	21.82	274.47	2.64	25.72
1e6e	17.44	263.02	3.83	21.22
1eaw	13.44	105.32	2.33	9.84
1ewy	15.55	198.00	2.96	16.14
1ezu	18.41	343.48	3.34	28.63
1f34	18.89	334.80	3.38	26.67
1f6m	18.39	260.07	3.10	22.33
1fle	13.87	125.53	2.03	11.89
1fq1	15.45	803.63	2.93	25.67
1gl1	12.94	141.48	2.00	28.49
1gxd	22.42	479.30	4.23	43.49
1hia	14.52	134.32	2.75	11.44
1ijk	19.06	315.03	3.18	26.49
1jiw	16.79	226.43	3.54	30.13
1jtg	15.68	179.72	2.79	17.02
1kkl	18.58	259.15	3.76	22.56
1m10	18.15	414.60	3.14	51.70
1mah	16.70	541.47	2.95	17.08
1n8o	17.14	247.50	2.81	21.17
1nw9	16.21	167.52	2.86	33.74
1oc0	15.91	128.75	2.45	16.57
1oph	15.90	333.18	3.77	29.47
1oyv	14.69	306.47	2.17	24.81
1ppe	12.60	73.58	1.97	6.50
1pxv	12.78	249.45	2.14	20.81
1r0r	12.12	71.53	1.96	6.66
1tmq	15.21	269.40	3.39	24.83
1udi	13.91	137.22	2.21	13.56
1yvb	19.83	181.30	2.78	39.90
1zli	18.05	669.10	3.25	46.85
2abz	13.02	166.20	2.16	13.58
2b42	18.17	192.30	3.36	26.60
2j0t	13.94	144.35	2.01	13.94
2mta	15.18	209.27	2.67	18.73
2o3b	14.19	176.68	2.19	16.38
2o8v	14.29	148.28	2.05	13.66
2oul	15.89	494.57	2.85	17.63
2pcc	14.32	175.65	2.45	16.09
2sic	14.58	167.47	2.91	15.19
2sni	12.92	123.20	2.17	11.48
2uuy	14.23	108.97	1.99	9.43
3sgq	12.62	250.78	1.78	7.10
4cpa	12.96	132.55	2.16	26.43
7cei	11.18	147.08	1.91	11.97
Average	15.39	232.15	2.67	20.19

The table shows execution times for the FMFT algorithm and PIPER when applied to 51 enzyme–inhibitor pairs from the Protein Docking Benchmark version 4.0. All runs used the standard PIPER energy function consisting of eight correlation terms. Running times for both serial and parallel versions of the algorithms were measured on Intel Xeon E5-2680 processors.