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Table 2 Performance differences among algorithms for the homopolymers of length 12, 24, 32.

From: An adaptive bin framework search method for a beta-sheet protein homopolymer model

Method Length E avg ± sd E min CPU Time avg Time med Time q 75 Time q 25 p – value
MC 12 -39 (± 0) -39 < 1 sec < 1 sec < 1 sec < 1 sec  
REMC 12 -39 (± 0) -39 < 1 sec < 1 sec < 1 sec < 1 sec  
PHAT 12 -39 (± 0) -39 < 1 sec < 1 sec < 1 sec < 1 sec  
BINMC 12 -39 (± 0) -39 < 1 sec < 1 sec < 1 sec < 1 sec  
MC 24 -109 (± 0) -109 5.0 min (± 4.1 min) 5.5 min 7.2 min 1.5 min 0.1230
REMC 24 -109 (± 0) -109 18.3 min (± 18.0 min) 16.3 min 19.4 min 4.3 min 0.0015*
PHAT 24 -109 (± 0) -109 8.7 min (± 8.2 min) 6.6 min 11.7 min 2.9 min 0.0039*
BINMC 24 -109 (± 0) -109 1.7 min (± 1.2 min) 1.8 min 2.7 min 0.5 min  
Method Length E avg ± sd Lowest E CPU Time avg E med E q 75 E q 25 p – value
MC 32 -158.1 (± 0.9) -161 4.3 min (± 8.4 min) -158 -158 -158 0.0155*
REMC 32 -158.2 (± 0.7) -161 4.5 min (± 8.6 min) -158 -158 -158 0.0185*
PHAT 32 -158.3 (± 0.9) -161 5.8 min (± 8.0 min) -158 -158 -158 0.0214*
BINMC 32 -158.9 (± 0.6) -161 23.0 min (± 20.1 min) -159 -159 -158  
  1. Comparison of the average energy level obtained and the average time required for the homopolymers of lengths N = 12, 24, 32 for the re-implemented MC, REMC, PHAT, and BINMC. The time cut-off used was 1 CPU hour on our 2.4 GHz reference machine, and all statistics were calculated from 10 independent runs. The temperature sets used for our implementations of MC, REMC and are the same as in Table 1. The p-values reported in the last column were determined using the Mann-Whitney U test to test the null hypothesis that the mean run-time (for N = 24) and the mean energies reached by the respective algorithm vs BINMC (within the same CPU cut-off time for N = 32), respectively, are identical [4]; p-values marked with an asterisk (*) correspond to cases in which the null hypothesis is rejected at a standard significance level of 0.05, and therefore indicate statistically significant performance differences.