Comparison of energies found by REMC and PERM for long biological sequences. The best and mean energy values found over 10 independent, one hour runs for each of the long biological sequences found in Supplemental Table 2 [see Additional file 1] is shown. The mean energy values reported for each instance is the average energy found amongst the 10 independent runs; the best energy is the lowest value found amongst the 10 runs. Notice that ground-state conformations have minimal free energy and therefore lower energy values are more desirable. In the 2D case (left side), PERM finds a best energy value lower than REMC in one instance and matched the best energy value found by REMC in two other instances. In the other 7 instances, REMC finds conformations with lower energies. In all instances, the average energy found was lower for REMC than PERM. In the 3D case (right side), REMC reports lower energies than PERM overall and on average for every instance.