A Parallel Framework for Multipoint Spiral Search in ab Initio Protein Structure Prediction

Table 7

The best and average contact energies obtained from 8 different approaches using Berrera et al. [25] 20×20 energy matrix. Rowwise bold-faced values are the winners for the corresponding proteins amongst the variants of spiral search (both single and parallel frameworks) and bold-italic-faced values are the winners for the corresponding proteins amongst all 8 approaches. For both energy and RMSD values, the lower the better.

Comparing all-atomic interaction energy and RMSD values
			State-of-the-art		Spiral search		Parallel spiral search (PSS) variants on energy model mixing										State-of-the-art
			CPU time 1 hr		CPU time 1 hr		CPU time 1 hr (4-threads × 15 minutes))										CPU time 1 hr
Protein details			1 × br-thread		1 × br-thread		4 × br-threads		3 × br-threads		2 × br-threads		1 × br-thread		0 × br-thread		br and hp based
			0 × hp-thread		0 × hp-thread		0 × hp-thread		1 × hp-thread		2 × hp-threads		3 × hp-threads		4 × hp-threads		single threaded
			LS-Tabu [10]		SS-Tabu		PSSB4H0		PSSB3H1		PSSB2H2		PSSB1H3		PSSB0H4		GA^+ [11]
Seq.	Size	H	Energy	RMSD	Energy	RMSD	Energy	RMSD	Energy	RMSD	Energy	RMSD	Energy	RMSD	Energy	RMSD	Energy	RMSD
4RXN	54	27	−156.32	6.29	−150.11	6.00	−142.22	5.23	−154.47	5.21	−156.94	5.11	−157	5.19	−157.25	5.17	−162.72	5.41
1ENH	54	19	−146.69	6.61	−143.01	5.88	−129.23	5.11	−146.88	5.09	−147.76	5.02	−148.58	4.93	−148.39	4.90	−151.65	5.22
4PTI	58	32	−198.42	7.07	−190.77	6.99	−175.52	6.41	−196.05	6.27	−197.33	6.38	−198.42	6.38	−198.3	6.37	−204.56	6.46
2IGD	61	25	−174.19	9.33	−163.87	8.50	−151.09	7.26	−171.74	7.26	−172.83	7.28	−173.89	7.33	−174.02	7.43	−176.83	7.81
1YPA	64	38	−239.98	7.53	−236.10	6.86	−214.60	6.00	−245.19	6.05	−248.43	5.93	−247.35	5.77	−248.54	5.86	−253.09	6.29
1R69	69	30	−204.17	6.47	−191.14	5.65	−175.61	5.14	−203.22	4.92	−204.81	4.85	−205.88	4.88	−207.06	4.78	−208.79	5.17
1CTF	74	42	−213.81	7.23	−197.85	5.63	−179.18	5.23	−218.38	5.21	−220.1	5.06	−222.23	5.02	−221.67	5.06	−225.42	5.28
3MX7	90	44	−311.56	8.18	−300.89	8.62	−257.49	7.87	−321.94	8.00	−324.09	7.8	−326.23	7.70	−325.55	7.64	−325.45	7.94
3NBM	108	56	−401.99	8.58	−380.12	6.95	−329.7	6.88	−409.5	6.12	−406.74	6.06	−412.96	6.06	−411.18	6.00	−419.25	6.46
3MQO	120	68	−455.27	8.86	−422.4	7.52	−336.74	7.39	−461.38	6.98	−465.02	6.83	−469.27	6.77	−467.38	6.67	−472.78	6.84
3MRO	142	63	430.29	10.02	−397.14	9.61	−313.85	8.74	−445.23	8.11	−450.68	7.93	−448.59	7.85	−452.04	7.71	−447.77	8.72
3PNX	160	84	−571.13	9.38	−502.29	9.55	−383.49	9.05	−586.68	8.73	−593.85	8.38	−595.99	8.45	−600.18	8.39	−592.25	8.51