[Biopython] Using DSSP to calculate SASA

[João Rodrigues]

Hi Ahmad,

DSSP, NACCESS, and MSMS are three very different programs that give
accessibility. NACCESS gives you per-atom and per-residue absolute and
relative accessibilities, which are very useful in some applications. DSSP
gives you absolute accessibilities per residue. MSMS gives you a solvent
exposure metric (in a way).

Relative means exactly that, it will divide whatever value you get from
DSSP by a standard value for each residue. You have three different scales
to choose from to normalize the values, whose papers are reference in the
documentation so you should look them up and see what exactly they refer
too and how those standard values were calculated.

If you want just the SASA, without any modification, just access the values
that the DSSP dictionary returns. If you want the relative accessibility,
access the key 'EXP_DSSP_RASA'.

NACCESS works only on Linux yes. But you have FREESASA, which should work
on Windows with a bit of effort, is actively maintained, and has the same
scale/references as NACCESS so it gives the same results (0.99 correlation).
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