The development of computational techniques to guide the experimental processes is an important step for the determination of the protein functions. The purpose of the activity here described is the characterization of the active sites in protein surfaces and their quantitative representation. A few pocket parameters like volume, travel depth, mouth area and perimeter, amplitude parameters, interfacial area ratio, summit density and mean summit curvature are hierarchically accessible through a concavity tree that topologically represents the entire protein molecule. This structural representation is particularly useful for the evaluation of binding pockets, the comparison of the morphological similarity and the identification of potential ligand docking.

Proteins pockets analysis and description

CANTONI, VIRGINIO;LOMBARDI, LUCA
2010

Abstract

The development of computational techniques to guide the experimental processes is an important step for the determination of the protein functions. The purpose of the activity here described is the characterization of the active sites in protein surfaces and their quantitative representation. A few pocket parameters like volume, travel depth, mouth area and perimeter, amplitude parameters, interfacial area ratio, summit density and mean summit curvature are hierarchically accessible through a concavity tree that topologically represents the entire protein molecule. This structural representation is particularly useful for the evaluation of binding pockets, the comparison of the morphological similarity and the identification of potential ligand docking.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11571/202608
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