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 protein-ligand 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 registration. Our main contribution is in the adoption of a controlled random search as a more efficient global optimization approach along with a new dissimilarity measure. The reported computational experience and comparison show viability of the proposed approach.Conclusions: Our method performs well to detect similarity in binding sites when this in fact exists. In the future we plan to do a more comprehensive evaluation of the method by considering large datasets of non-redundant proteins and applying a clustering technique to the results of all comparisons to classify binding sites. © 2010 Bertolazzi et al; licensee BioMed Central Ltd.
A global optimization algorithm for protein surface alignment / Bertolazzi, P.; Guerra, C.; Liuzzi, G.. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 11:1(2010), p. 488.
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|Titolo:||A global optimization algorithm for protein surface alignment|
|Data di pubblicazione:||2010|
|Citazione:||A global optimization algorithm for protein surface alignment / Bertolazzi, P.; Guerra, C.; Liuzzi, G.. - In: BMC BIOINFORMATICS. - ISSN 1471-2105. - 11:1(2010), p. 488.|
|Appartiene alla tipologia:||01a Articolo in rivista|