Analysis of ligand binding sites using alpha shapes

Protein-ligand interaction is important in drug development and protein design. Previous studies focused on the detection of the potential ligand binding sites but lack of analysis of the true binding sites on the protein. In this work, we use alpha shape models to represent the surface of the protein structure and extract surface patches to study the ligand binding sites. Analysis is performed on X-ray crystallography data of protein-ligand structures. The results show that geometric properties play a significant role in the positioning of ligand molecule in protein-ligand interaction.