What is the buriedness of an amino acid?

• Is a measure based on the proximity of the amino acid to the surface of the protein.
• The surface is modeled by the convex hull of the atomic coordinates of the protein.
• Formally, if we let amino acid $r$ be composed of three atoms $a_1, a_2, a_3$ and $dist(a)$ be the shortest distance of an atom $a$ to the convex hull of the protein, then the buriedness of $r$ is equal to $(dist(a_1) + dist(a_2) + dist(a_3))/3$.

Why bother with buriedness when we have the ASA?

• Buriedness by definition does not have 0 values, as opposed to the accessible surface area. This allows to a comparison between midly buried to buried to very buried residues.

How to use the script?

To compute the buriedness in a protein, use the pdb file of the structure, suppose it is called file.pdb. Just type in the terminal:

$ python buriedness.py file.pdb > output.csv

Install

Clone the repository and listo!

$ git clone https://github.com/rodogi/buriedness.git

Requirements

• biopython
• scipy and numpy
• python > 2.7 or > 3.6

Licence

• GNU General Public License v3.0