The Wilcoxon signed-rank test of energy difference distributions (Table ) showed that uniform random search is significantly different from BOA with EI and LCB (p-value 0.01) for all numbers of rotatable bonds. Note that the sample sizes of the sets of molecules with one and two rotatable bonds are small, and we combined these with molecules having three rotatable bonds for the statistical test. This gave more reliable test results. For the EI-LCB pair, we obtained a large p-value except for molecules with one to three rotatable bond (p-value of 0.02). Thus we found no evidence to reject the null hypothesis that the results for EI and LCB come from the same distribution. Furthermore, we assessed the variation in energies found by BOA. In particular, we computed the maximum variation for each molecule, by extracting the lowest energy conformation found in each trial and computing the maximum difference in energy among these conformations. The results are summarized in Additional File 3. We observed a smaller variation in BOA than uniform search. The variation increases exponentially in uniform search while the variation increases gradually as the number of rotatable bonds increases in BOA search. The median reaches approximately 9 kcal/mol for molecules with six rotatable bonds in BOA search with EI and LCB. The range is larger in BOA with LCB than BOA with EI, except for molecules with five rotatable bonds.