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

Table 5

For 12 large sized proteins, the three different sets of excremental data—(i) our parallel local search framework (PSS), (ii) the tabu guided spiral search (SS-Tabu), and (iii) the genetic algorithms (GA⁺). The RI Columns present the relative improvements of parallel local search over the single-thread local search and the genetic algorithm. The RI is calculated on the average energy values.

			Our approach		The current state-of-the-art approaches
			(Four threads)		(Single thread)
Protein Info.			1.25 hrs × 4 = 5 hrs		5 hrs × 1 = 5 hrs
			PSS		SS-Tabu [9]			GA^+ [8]
Seq	Size	LBFE	Best	Avg (𝐸𝑡)	Best	Avg (𝐸𝑟)	RI	Best	Avg (𝐸𝑟)	RI
F180_1	180	−378	−359	−344	−357	−340	11%	−351	−341	8%
F180_2	180	−381	−364	−352	−359	−345	19%	−362	−346	17%
F180_3	180	−378	−368	−356	−362	−353	12%	−361	−350	21%
R1	200	−384	−366	−353	−359	−345	21%	−355	−346	18%
R2	200	−383	−368	−355	−358	−346	24%	−360	−346	24%
R3	200	−385	−369	−353	−365	−345	20%	−363	−344	22%
3mse	179	−323	−296	−285	−289	−280	12%	−290	−279	14%
3mr7	189	−355	−332	−319	−328	−313	14%	−328	−316	8%
3mqz	215	−474	−430	−414	−420	−402	17%	−427	−410	6%
3no6	229	−455	−429	−407	−411	−391	25%	−420	−400	13%
3no3	258	−494	−422	−404	−412	−393	11%	−421	−402	2%
3on7	279	n/a	−516	−500	−512	−485	n/a	−515	−485	n/a