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Surface analysis

In our surface topography analysis we have used the fractal atomic density measure of Kuhn et al.kuhn:fractals to determine local curvature on a molecular surface. This quantity is calculated for each surface point as the slope of the log-log plot (by linear regression) of the number of all protein atom (not just surface atom) centres contained within a 1Å thick spherical shell versus the internal radius of this shell as it varies between 0 and 10Å. The fractal atomic density of a point on a perfectly flat protein surface would be 2.0 because the number of atom centres within each shell would be proportional to the sphere's surface area (which is proportional to the radius raised to the power of 2.0). Convex and concave surface points give fractal atomic densities less than and greater than 2.0 respectively.



Copyright Bob MacCallum - DISCLAIMER: this was written in 1997 and may contain out-of-date information.