[Biopython] Calculating Buried and Surface Residues

[João Rodrigues]

Hello Jordan,

If you can get your hands on
NACCESS<http://www.bioinf.manchester.ac.uk/naccess/> that
will do the trick. Biopython PDB module has a wrapper for this program
which makes it pretty easy to use.

Another alternative is to use the Half Sphere Exposure measure that is
built-in Biopython and described
here<http://en.wikipedia.org/wiki/Half_sphere_exposure>
.

Either way gives you per-residue information.

Best,

João [...] Rodrigues
http://nmr.chem.uu.nl/~joao



2011/11/24 Willis, Jordan R <jordan.r.willis at vanderbilt.edu>

> Hello Biopython,
>
> I was wondering if anyone had a script, knew of a script, API, web-server,
> Pymol example, etc. to do something I have seen in so many papers but can't
> seem to find a way to do it. That is, given a PDB, calculate which residues
> are considered buried, and which ones are considered solvent exposed. If
> this is easy in Biopython, I would love to use it. Otherwise, if anyone
> knows anything out there for this task, please let me know.
>
> Thanks so much!
>
> Jordan
>
>
>
>
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