Accessible Surface

-Continuous sheet defined by the position of the center of the center of the probe as the solvent probe is rolled over the protein

-Is not smooth or continuously differentiable

-Two ways of calculating accessible surface

1. Lee and Richards (1970)
   • Slice protein into sections
   • Each atom is given radius = Van der Waals radius + solvent probe radius
   • For each atom, find the circle corresponding to the intersection of its sphere with the sectioning plane
   • Remove parts of each circle that are occluded by other circles
   • Get surface of each atom by multiplying non-occluded arc length by the sectioning width
   • Add the surfaces of all atoms together to get the total surface
2. Shrake and Rupley (Dot method)
   • Each atom surrounded by sphere of evenly spaced dots (92 dots/atom)
   • Dots contained in another atom's sphere of dots are removed

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