Application of promolecular ASA densities to graphical representation of density functions of macromolecular systems.

X Gironés, R Carbó-Dorca, P G Mezey

Institute of Computational Chemistry, University of Girona, Campus Montilivi, 17071 Girona, Catalonia, Spain.

Journal of molecular graphics & modelling 2001

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In this article we report the application of the Promolecular Atomic Shell Approximation (Promolecular ASA) to the graphical representation of the density function (DF) of large macromolecular systems. Promolecular ASA DF, constructed from previously computed and fitted atomic densities, provides a fast and practical representation of Molecular IsoDensity Contours (MIDCOs). These representations can be extended to macromolecular systems composed by > 1000 atoms easily and with low computational costs, allowing the visualization of protein DF. The method is at first presented with a small molecule (2,4,6-trinitrophenol), comparing the resulting ASA MIDCOs with direct ab initio contours. For macromolecular tests the Promolecular ASA densities are also applied to the generation of macromolecular density surfaces of two proteins: myoglobin (2541 atoms) and gene V protein (1362 atoms).

Citation

X Gironés, R Carbó-Dorca, P G Mezey. Application of promolecular ASA densities to graphical representation of density functions of macromolecular systems. Journal of molecular graphics & modelling. 2001;19(3-4):343-8