Calculations of protein volumes: sensitivity analysis and parameter database | Zendy

Jerry Tsai | Zendy; Mark Gerstein | Zendy

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Calculations of protein volumes: sensitivity analysis and parameter database

Author(s) -

Jerry Tsai,

Mark Gerstein

Publication year - 2002

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/18.7.985

Subject(s) - polyhedron , voronoi diagram , van der waals radius , set (abstract data type) , plane (geometry) , atom (system on chip) , volume (thermodynamics) , sensitivity (control systems) , van der waals force , selection (genetic algorithm) , quality (philosophy) , materials science , chemistry , crystallography , mathematics , computer science , physics , combinatorics , thermodynamics , geometry , molecule , organic chemistry , quantum mechanics , electronic engineering , artificial intelligence , embedded system , engineering , programming language

The precise sizes of protein atoms in terms of occupied packing volume are of great importance. We have previously presented standard volumes for protein residues based on calculations with Voronoi-like polyhedra. To understand the applicability and limitations of our set, we investigated, in detail, the sensitivity of the volume calculations to a number of factors: (i) the van der Waals radii set, (ii) the criteria for including buried atoms in the calculations or atom selection, (iii) the method of positioning the dividing plane in polyhedra construction, and (iv) the set of structures used in the averaging.

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