Adepth: A method to compute the depth of atoms in proteins.

Chen S.-w.W. and Pellequer J.-L. (2013) Adepth: new representation and its implications for atomic depths of macromolecules. Nucl. Acids Res. 41: W412-W416.

Go to the Adepth website.

We applied the signed distance function (SDF) for representing the depths of atoms in a macromolecule. The calculations of SDF values were performed on grid points in a rectangular box that accommodates the macromolecule. The depth for an atom inside the molecule was then obtained as a result of tri-linear interpolation of SDF values at the nearest grid points surrounding the atom. Theoretical concept and computational development performed by Wendy Chen.

Adepth allows you to:

  • 1) Calculate accurately the depth of any atom within a macromolecular structure
  • 2) Provide an extrusion (skin) of a macromolecular structure
  • 3) Generate of pseudo-2D convolution map, highlighting the effect of AFM tips on single molecules