Nucleic Acid Binding Energy Funnel on Protein Surface
When we plot the prediction score of nucleic acid binding score on protein surface, it is possible to show certain energy funnel that focus on the core binding region, while neighboring regions are less likely to binding nucleic acid. Farther away from the binding core, lower the score is.
Ideally, we can correlate the prediction score with the distance from the residue to its nearest binding core. However, it is difficult to define the binding core and to measure surface distance. Approximately, we can use minimum distance from a residue to nucleic acid instead.
We can find such an energy funnel is very similar to the energy funnel of protein folding and protein-nucleic acid docking.
Still, such energy funnels cannot guarantee that funnels for different proteins are identical Ref. We can also use Pearson correlation coefficiency to stand for the correlation between prediction score and minimum distance to nucleic acid. Higher correlation coefficiency generally means better energy funnel representation.