Diffusion accessibility gives a measure of surface
accessibility that is longer range in
nature than ordinary solvent accessibility. The idea of diffusion accessibility
was introduced several years ago (Yeates, TO (1995)
Algorithms for Evaluating the Long-range Accessibility of Protein Surfaces.
J Mol Biol 249(4): 804-15). Diffusion accessibility is a measure of how easily
or frequently a specific point on a surface would capture a hypothetical diffusing
(or randomly-walking) probe that is captured upon its first encounter with any part of a surface.
Naturally, parts of a surface that are solvent-exposed in the traditional sense but lie in a deep
surface depression will capture the probe only rarely, since the probe will more often encounter
another part of the surface first. The results of a diffusion accessibility calculation can be
useful in quantitatively evaluating potential binding regions of a protein surface, and are particularly
useful in visualization. Even the most widely used graphics programs for visualizing
proteins and their surfaces generally do not produce images that make the depth and character of
protein surfaces very obvious. Using the diffusion accessibility to color a surface can add
substantially to the depth cues and can produce a better appreciation of a surface, particularly those
regions likely to be involved in binding.
As discussed in the 1995 paper, the best way to calculate diffusion
accessibility is to cast it as a problem in steady-state diffusion, and solve the resulting (Poisson) equations
on a 3D grid. This website performs that calculation on an uploaded PDB file.
The calculation is performed on the server side and can be accessed here. The program returns
another pdb file that contains a normalized value of the diffusion accessibility for each atom in the
temperature factor (B factor) column.
The best way to use that information to color your images is to
use PyMol to view the new PDB file, and then color it using a PyMol script specially
written for that purpose. The script and its usage
For the analysis of large proteins, it is recommended that the diffusion accessibility program be downloaded and run on a local machine. The program is available here.
Frank Pettit was instrumental in translating the diffusion accessibility code to C and implementing the calculation
in the EZProt package. Yingssu Tsai was responsible for developing the web server. Tom Holton maintains the server.