05
How to Calculate Accessible Surface Area
- Lee & Richards algorithm (first method, 1970)
- Pick an arbitrary direction from which to view the protein.
Slice it into many sections perpendicular to this direction.
- In each section, cycle over all the atoms. Each atom is represented as a sphere with
a radius that is the sum of its VDW radius plus that
of a probe solvent -- i.e. 1.4 for water.
- For each atom determine the circle corresponding to the
intersection of this sphere with the sectioning plane. Remove all
parts (i.e. arcs) of this circle occluded by the circles of other
atoms.
- Multiply the total amount of non-occluded arc length by the
sectioning width to get the surface area for atom. Sum over all atoms
and all sections to get total area.
- Shrake & Rupley algorithm (easier)
- Surround each atom with sphere
of uniformly spaced dots (e.g. 92).
- Remove dots contained in other atoms spheres. Total number
of remaining dots is accessible surface.