Evaluation of existing cavities. We sequentially perform selections of cavities based on pairs of amino acids. A typical cavity for each selection is shown in the top-left corner and marked by the green circle in the temporal scatterplot. Left: We can see that cavities formed by Ile171 and Asp190 are quite correlated with respect to the content of negatively charged amino acids. The same holds for amino acids Ile1 and Asp190, but only for graphs containing both, i.e., 1&190. Right: We found that there is a higher number of cavities formed either by Ser176 or by Val193, 176v191, than by both of them, 176&191. Note that the hydrophobicity of all the cavities is much smaller than in the cavities formed in the left side. We might see similar cavity occurrences when selecting cavities formed by Ser173 or by Val193 (176 ∨ 193) while cavities are more hydrophobic. Importantly, in the simulation section, we do not find any cavity when querying both Ser173 and Val193 (176&193).
Parulek et al. BMC Bioinformatics 2013 14(Suppl 19):S4 doi:10.1186/1471-2105-14-S19-S4