title: A Fast Algorithm to Compute Conical Pockets in Proteins. Application to the Structural Characterization of γ-Carbonic Anhydrases.
abstract: Some major proteins families, such as carbonic anhydrases (CAs), have a conical cavity at the active site. No algorithm was available to compute conical cavities, so we needed to design one. The fast algorithm we designed let us show on a set of 717 CAs extracted from the PDB database that γ-CAs are characterized by active site cavity cone angles significantly larger than those of α-CAs and β-CAs: the generatrix-axis angles are greater than 60° for the γ-CAs while they are smaller than 50° for the other CAs. Free binaries of the CONICA software implementing the algorithm are available through a software repository at http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html.
authors.affiliation: Université Paris Diderot, MTi (INSERM UMR-S 973), 35 rue Hélène Brion, F-75013, Paris, France.|Université Paris Diderot, E-pôle de génoinformatique (IJM, CNRS UMR 7592), 15 rue Hélène Brion, F-75013 Paris, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Petitjean
mesh_terms: D000465:Algorithms; D002256:Carbonic Anhydrases / Q000737:chemistry* / Q000378:metabolism*; D030562:Databases, Protein
chemical_list: D002256:Carbonic Anhydrases
keywords: Algorithm; Delaunay triangulation; carbonic anhydrases; conical protein pockets