A global optimization algorithm for protein surface alignment

Background: A relevant problem in drug design is the comparison and recognition of protein binding sites. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site since the conformation, size and chemical composition of the protein surface are all relevant for the interaction with a specific ligand. Several matching strategies have been designed for the recognition of proteinligand binding sites and of protein-protein interfaces but the problem cannot be considered solved. Results: In this paper we propose a new method for local structural alignment of protein surfaces based on continuous global optimization techniques. Given the three-dimensional structures of two proteins, the method finds the isometric transformation (rotation plus translation) that best superimposes active regions of two structures. We draw our inspiration from the well-known Iterative Closest Point (ICP) method for three-dimensional (3D) shapes registrat...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Paola Bertolazzi, Concettina Guerra, Giampaolo Liuzzi
• Keywords: Binding Sites, BMCBI 2010, Protein, Proteinligand Binding Sites