Identifying Calcium-Binding Sites with Oxygen-Carbon Shell Geometric and Chemic Criteria-A Graph-Based Approach

Identifying calcium-binding sites in proteins help acknowledge protein functions. We thus developed a graph theory and geometry approach to improve the accuracy for predicting calcium-binding sites, we enhance our previous approach at a high level to find biggest local oxygen clusters with a graph algorithm to find maximal cliques and propose a new geometric criterion embedding the bidentate property to filter non calcium-binding oxygen clusters. In addition, we apply some motifs of residue combinations as another filter to exclude non calcium-binding oxygen clusters possibly formed by hydrogen bonds and obtain higher site selectivity without trading off site sensitivity. The experiments demonstrate good predictive performance on both old and new datasets.