A Fast Algorithm to Compute Conical Pockets in Proteins. Application to the Structural Characterization of γ-Carbonic Anhydrases

Michel Petitjean

doi:10.1002/minf.201600155

A Fast Algorithm to Compute Conical Pockets in Proteins. Application to the Structural Characterization of γ-Carbonic Anhydrases

Mol Inform. 2017 Oct;36(10). doi: 10.1002/minf.201600155. Epub 2017 Apr 12.

Author

Michel Petitjean^{1

2}

Affiliations

¹ Université Paris Diderot, MTi (INSERM UMR-S 973), 35 rue Hélène Brion, F-75013, Paris, France.
² Université Paris Diderot, E-pôle de génoinformatique (IJM, CNRS UMR 7592), 15 rue Hélène Brion, F-75013 Paris, France.

PMID: 28402608
DOI: 10.1002/minf.201600155

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.

Keywords: Algorithm; Delaunay triangulation; carbonic anhydrases; conical protein pockets.

MeSH terms

Algorithms*
Carbonic Anhydrases / chemistry*
Carbonic Anhydrases / metabolism*
Databases, Protein

Substances

Carbonic Anhydrases