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BMCBI
2010

A global optimization algorithm for protein surface alignment

8 years 11 months ago
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...
Paola Bertolazzi, Concettina Guerra, Giampaolo Liu
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Paola Bertolazzi, Concettina Guerra, Giampaolo Liuzzi
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