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
