[Bioperl-l] re: buried surface calculation

[Neil Saunders]

hi Osmany,

There are a couple of solutions to your problem.  First, you will need 
to process your PDB file with something that calculates the required 
surface areas.  You may be able to use DSSP for that, which would be 
nice because Bioperl includes a module for parsing DSSP output.  It is 
documented here:

http://doc.bioperl.org/releases/bioperl-1.4/Bio/Structure/SecStr/DSSP/toc.html

The method:
$solv_acc = $dssp_obj->resSolvAcc( RESIDUE_ID );

returns the solvent-accessible area of a residue, so if you knew the 
total surface area, you could calculate what was buried.

Another option might be to use the program naccess:

http://wolf.bms.umist.ac.uk/naccess/

There is no Bioperl module for this output so far as I know (it's 
something I'd like to write one day).  But the output (a .rsa file) is 
quite easy to parse, as it is mostly space-delimited columns.

I wrote a few scripts to process naccess output some years ago.  You 
might get some ideas from them, see 'surface_charge.pl' and 
'parse_nacc_core2.pl' at my CVS server:

http://psychro.bioinformatics.unsw.edu.au/cgi-bin/viewcvs.cgi/GenRes2003/scripts/#dirlist

I knew very little Perl when I wrote these so they are embarassingly 
awful, but they may give you an idea of how .rsa files can be parsed.


Neil
-- 
 School of Biotechnology and Biomolecular Sciences,
 The University of New South Wales,
 Sydney 2052,
 Australia

http://psychro.bioinformatics.unsw.edu.au/neil/index.php