Hydrophobic surface calculation

Simon Brocklehurst smb at bioch.ox.ac.uk
Thu Oct 24 06:42:07 EST 1996


Juergen Pleiss wrote:
> 
> Dear colleagues,
> 
> we are searching for a program which calculates the total hydrophobic,
> solvent accessible surface of a protein or a small molecule.
> It should read in a PDB file and output the surface area in Angstrom**2,
> which is hydrophobic _and_ solvent accessible (hydrophobicity defined by
> any of the hydrophobicity scales, solvent defined by a probe radius).
> Ideally, the program uses a user editable parameter file, which
> equivalences atom names (as given in the PDB file), VdW radius and
> hydrophobicity index, so that the user can add atoms to it.
> I would be glad if you could point me to such a program.
> 
> Thank you for your help,
> Juergen Pleiss
> 
> ================================================================================
> 
> Dr.Juergen Pleiss
> Institute of Technical Biochemistry
> University of Stuttgart          Email:jpleiss at tebio1.biologie.uni-stuttgart.de
> Allmandring 31                   Phone:(+49)-711-685-3191
> D-70569 Stuttgart, Germany       Fax:  (+49)-711-685-3196
> W3 home page:  http://www.itb.uni-stuttgart.de:8080/

If you have an SGI, you can do most of what you want with NAOMI.  Here
is
an extract from the user guide showing how to get overall figures for
a whole molecule (you can of do more detailed calculations too using
different
commands).
You can't put in your own atom types though.

------------------------------------------------

The command: 

        table total_access

outputs information on the total solvent accessible surface of the
protein. Example output is: 


NAOMI>OUTPUT Total Solvent Accessible Surface of Protein
NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAOMI>OUTPUT Total               6242 A^2
NAOMI>OUTPUT    Main-chain       1393 A^2     22 %
NAOMI>OUTPUT    Side-chain       4849 A^2     78 %
NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAOMI>OUTPUT Total hydrophobic   3318 A^2     53 %
NAOMI>OUTPUT    Main-chain        677 A^2     20 %
NAOMI>OUTPUT    Side-chain       2640 A^2     80 %
NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NAOMI>OUTPUT Total hydrophilic   2924 A^2     47 %
NAOMI>OUTPUT    Main-chain        715 A^2     24 %
NAOMI>OUTPUT    Side-chain       2209 A^2     76 %
NAOMI>OUTPUT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


More info in the on-line User Guide at the web site...

         http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html


-- Simon

----------------------------------------------------------
Simon M. Brocklehurst
Dept Biochemistry
University of Oxford
UK




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