Three-dimensional computation of atom depth in complex molecular structures | Zendy

D. Varrazzo | Zendy; Andrea Bernini | Zendy; Ottavia Spiga | Zendy; Arianna Ciutti | Zendy; S. Chiellini | Zendy; Vincenzo Venditti | Zendy; Luisa Bracci | Zendy; Neri Niccolai | Zendy

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Three-dimensional computation of atom depth in complex molecular structures

Author(s) -

D. Varrazzo,

Andrea Bernini,

Ottavia Spiga,

Arianna Ciutti,

S. Chiellini,

Vincenzo Venditti,

Luisa Bracci,

Neri Niccolai

Publication year - 2005

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti444

Subject(s) - atom (system on chip) , surface (topology) , measure (data warehouse) , molecule , molecular physics , folding (dsp implementation) , volume (thermodynamics) , chemical physics , physics , chemistry , algorithm , crystallography , materials science , computer science , geometry , mathematics , quantum mechanics , data mining , engineering , electrical engineering , embedded system

For a complex molecular system the delineation of atom-atom contacts, exposed surface and binding sites represents a fundamental step to predict its interaction with solvent, ligands and other molecules. Recently, atom depth has been also considered as an additional structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the 3D character of depth is largely lost. In the present study, a new approach is proposed to calculate atom depths in a way that the molecular shape can be taken into account.

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