It should be emphasized that GROUPSIM predicts SDPs for the alignment, not just for Swf1, so some of these positions may be important specificity determinants for other PATs.
The Venn diagrams may provide a generally useful tool to highlight the most important specificity determinants for rational redesign.
Nonetheless, the model should account for two important specificities that emerge from the historical trajectories of migration and the resulting regimes.
This indicates that although the Ser/Pro and Leu/Gln mutations are important for-specificity for 17α-hydroxy-steroids, other amino acids influence the role of Leu and Gln on the MR and GR, respectively, in this response.
In HucR and PecS, however, this residue is also important for conferring specificity for the negatively charged urate.
From these results it appears that these two tests could be use to complement each other: mannan has an important contribution to specificity for low BDG values, while high BDG levels have improved sensitivity and specificity.
Clearly Trp107f is not the only residue important for specificity – a major point of our paper – but the same is true of the "traditional" specificity residue at position 102, which is at best necessary but insufficient for determining substrate specificity.
Hydrogen bonds predicted to be important for specificity based on structural considerations do not always turn out to be significant to binding in post facto analyses of molecular dynamics trajectories, which treat thermal averaging, solvent, and counterion effects rigorously.
Moreover, cation-π interactions are important for specificity and stability during protein association [54], [57].
GROUPSIM assigns each position or column in the alignment, a score which ranges from 0 to 1, and indicates how likely it is to be important for specificity determination.
