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

Table 4

For 9 medium 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.			0.5 hrs × 4 = 2 hrs		2 hrs × 1 = 2 hrs
			PSS		SS-Tabu [9]			GA^+ [8]
Seq	Size	LBFE	Best	Avg (𝐸𝑡)	Best	Avg (𝐸𝑟)	RI	Best	Avg (𝐸𝑟)	RI
F90_1	90	−168	−168	−166	−168	−167	0%	−168	−166	0%
F90_2	90	−168	−168	−166	−167	−164	50%	−168	−165	33%
F90_3	90	−167	−167	−165	−167	−165	0%	−167	−164	33%
F90_4	90	−168	−168	−166	−168	−165	33%	−168	−165	33%
F90_5	90	−167	−167	−165	−167	−165	0%	−167	−166	0%
S1	135	−357	−355	−350	−355	−347	30%	−355	−348	22%
S2	151	−360	−356	−351	−354	−347	31%	−356	−349	18%
S3	162	−367	−360	−354	−359	−350	26%	−361	−349	28%
S4	164	−370	−364	−358	−358	−350	40%	−364	−352	33%