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

Petitjean Michel | Zendy

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

Author(s) -

Petitjean Michel

Publication year - 2017

Publication title -

molecular informatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 0.481

H-Index - 68

eISSN - 1868-1751

pISSN - 1868-1743

DOI - 10.1002/minf.201600155

Subject(s) - conical surface , protein data bank (rcsb pdb) , software , algorithm , set (abstract data type) , computer science , generatrix , computational science , chemistry , mathematics , geometry , stereochemistry , programming language

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.

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