A cavity formed by Ile1, Ile171 and Asp190 (1&171&190). Left: An illustration of of the same cavity in different time steps (533,537,538,539 and 541) marked by the black circle in the temporal scatterplot. We performed specification of 1&171&190 as a continuation of the analysis started in Figure 7, which shows that the cavity might be formed by all three amino acids. The cavity is located deep inside PR3 and we have to use the ICP to show it. Bottom-right: It is easy to see that the chemical properties of the cavity are very stable over entire simulation, where hydrophobicity prevails over polarity.
Parulek et al. BMC Bioinformatics 2013 14(Suppl 19):S4 doi:10.1186/1471-2105-14-S19-S4