Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
Figure 5
Comparison of different versions of ConCavity.
ConCavity provides a general framework for binding site prediction. We use Ligsite+ -based ConCavity as representative, but it is possible to use other algorithms in ConCavity. This figure compares the PR curves for three versions (ConCavityL, ConCavityP, ConCavityS )---each based on integrating sequence conservation with a different grid creation strategy (Ligsite+, PocketFinder+, or Surfnet+). All three versions perform similarly, and all significantly outperform the methods based on structure analysis alone (dashed lines). These conclusions hold for both ligand binding pocket (A) and ligand binding residue (B) prediction.