Analysis of surface structures of hydrogen bonding in protein–ligand interactions using the alpha shape model

Hydrogen bonding provides useful information for the study of protein–ligand interactions. However, the physical role that a hydrogen bond plays and its 3D surface characteristics in protein–ligand interaction are still not well understood. We apply the 3D alpha shape model to reconstruct the interface of a protein–ligand structure and use solid angles at interface atoms to represent the surface geometric properties of a hydrogen bond. The result shows that 77.2% of the hydrogen bonds show complementary geometric patterns and 95.0% of the protein–ligand complexes contain at least one such hydrogen bond.