A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand bindin

Background: An accurate description of protein shape derived from protein structure is necessary to establish an understanding of protein-ligand interactions, which in turn will lead to improved methods for protein-ligand docking and binding site analysis. Most current shape descriptors characterize only the local properties of protein structure using an all-atom representation and are slow to compute. We need new shape descriptors that have the ability to capture both local and global structural information, are robust for application to models and low quality structures and are computationally efficient to permit high throughput analysis of protein structures. Results: We introduce a new shape description that requires only the Cα atoms to represent the protein structure, thus making it both fast and suitable for use on models and low quality structures. The notion of a geometric potential is introduced to quantitatively describe the shape of the structure. This geometric potential...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Lei Xie, Philip E. Bourne
• Keywords: Binding Sites, BMCBI 2007, Geometric Potential, Protein Structure