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. © 2012 Elsevier B.V. All rights reserved.