Authors:
Virginio Cantoni
;
Riccardo Gatti
and
Luca Lombardi
Affiliation:
University of Pavia, Italy
Keyword(s):
Protein-ligand docking, Curvature analysis, Concavity tree, Travel depth, Pocket mouth area and perimeter.
Related
Ontology
Subjects/Areas/Topics:
Bioinformatics
;
Biomedical Engineering
;
Genomics and Proteomics
;
Structural Bioinformatics
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.