A topology approach towards modeling activities and properties on a biomolecular surface

Geometric features of protein surfaces play an important role in the identification of biomolecular structures, functions, and interactions. These features have been crucial in predicting binding sites for protein-ligand or protein-protein interactions. This paper introduces simplicial complexes and discrete Morse theory to extract important geometric information on the protein surface. Using the extracted geometric information, we provide possible intermediate conformations around the protein surface as the ligand travels to the binding site. We compare the efficiency of our method with the state-of-art-method in terms of computation time and total complexes needed to generate the topological structure of the protein surface. We also show comparable relevance of the binding affinity of our method in relation to the known native protein binding site.