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Analytical molecular surface calculation
Author(s) -
Connolly M. L.
Publication year - 1983
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889883010985
Subject(s) - surface (topology) , van der waals surface , van der waals force , spheres , radius , torus , molecular graphics , van der waals radius , molecule , raster graphics , chemistry , geometry , physics , computer graphics , mathematics , computer graphics (images) , computer science , organic chemistry , computer security , astronomy
A computer algorithm is presented for calculating the part of the van der Waals surface of molecule that is accessible to solvent. The solvent molecule is modeled by a sphere. This sphere is, in effect, rolled over the molecule to generate a smooth outer‐surface contour. This surface contour is made up of pieces of spheres and tori that join at circular arcs. The spheres, tori and arcs are defined by analytical expressions in terms of the atomic coordinates, van der Waals radii and the probe radius. The area of each surface piece may be calculated analytically and the surface may be displayed on either vector or raster computer‐graphics systems. These methods are useful for studying the structure and interactions of proteins and nucleic acids.