Hydrophobic surface calculation

Juergen Pleiss jpleiss at tebio1.biologie.uni-stuttgart.de
Fri Nov 8 04:32:11 EST 1996


> 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


Many thanks to all who have responded. 

Here is the summary :



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

From: merckel at max.mpibp.uni-frankfurt.de

Hi Juergen,
NACCESS will give you waht you want.

http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html

It reads PDB files and generates per atom and per residue
surface areas. With grep and awk you can easily get the
areas relative to any desired atom type. The code is 
freely available.
HTH
Mike

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

From: Stefan Grzybek <grzybek at ruf.uni-freiburg.de>

Hallo Juergen Pleiss,

Hast Du schon mal was von Grasp gehoert? Mit diesem Programm kann man sehr
schoen Molekueloberflaechen berechnen und darstellen. Allerdings ist es nur
fuer Silicon Graphics verfuegbar. Es verwendet Parameterdateien fuer
Atomradien und Partialladungen (da es auch fuer elektrostatische Rechnungen
geeignet ist) und man kann auch beliebige andere Daten, wie z.B deine
Hydrophobizitaets-Daten als Werte aus den B-Faktor und Besetzungs-Werten
einer PDB-Datei einlesen. Mit allen moegliche Daten kann man innerhalb des
Programmes auch Rechnungen durchfuehren. Es kann auch die Flaeche
beliebiger Oberflaechenelemente berechnen - genau das was Du brauchst.

Leider ist Grasp nicht kostenlos (auch nicht fuer Hochschulen).

Fuer weitere Informationen siehe:
http://tincan.bioc.columbia.edu/Lab/grasp

Stefan

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

From: Zhan-yang Zhu <zhu at gallery.stanford.edu>

Try to contact Andrej Sali at Rockefeller University by 

     Name: Sali, Andrej
   E-mail: sali at rockvax.rockefeller.edu

He has the program to do what you want, I think.

Good luck!

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

From: Alessandro Giolitti <lns at dada.it>


You could probably work a bit through GRID, by Peter Goodford, using the
hydrophobic probe.

Alessandro Giolitti

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

From: Simon Brocklehurst <smb at bioch.ox.ac.uk>

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

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

From: Richard Macdonald <richard at msi.com>


The Insight II program from our company, MSI, does most 
(or all) of what you want.

There is a command within Homology and NMR_Refine modules that
will calculate the accessible surface area, and will
separate the areas into polar/nonpolar (which is another
measure of hydrophobicity).  The command is called 
ProStat/Access_Surf (for protein statistics/accessible
surface).  InsightII can be run in graphics mode,
or as a command line program.  The results can be presented
in a table (graphics mode), or simply printed to the shell
(command line mode).

The Access_Surf command works on default atom names, radii, 
and polarity, but all these can all be overridden by specifying 
an input file. The file contains the atom names and their values, 
with wild-carding allowed.  The mechanism was designed to allow
any atomic model (full atom model, or united atom model) to be
accomodated.  Example input files for several united atom models
are given in the User Guide.

Now all you need to do is find someone who has InsightII!!

-- richard

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

From: mike at dino.fold.fccc.edu (J. Mike Sauder)

        I assume you're looking for a freeware program?  
        You might want to take a look at NAOMI:

http://www.ocms.ox.ac.uk/~smb/Software/N_details/naomi.html
or
http://molbio.info.nih.gov/modeling/software_list/naomi/doc.html

-- Mike S. (m_sauder at fccc.edu) http://www.fccc.edu/research/labs/roder/

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

From: friedman at cgl.ucsf.EDU

Hello, I've done this using the program MS, which calculates
molecular surfaces from pdb files.  I then use an 'awk' 
script to run through the MS generated surface file and
add all the surface elements for each atom type.  The total
carbon surface is a reasonable estimate of hydrophobic 
surface.  
Hope this helps,

Simon

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

From: Finn Drablos <drablos at linus.unimed.sintef.no>

It is possible to do this with Grasp. You may need a bit work to
get started, but as you are able to control Grasp via scripts,
much of the hard work can be made automatic. We have used this
to look at the amount of surface area of hydrophobic nature,
or with electrostatic potential within a certain range, or involved
in hydrogen bonding etc, for various molecules and complexes.
---
Finn Drablos         

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

From: jose at lpoly.bioc.cwru.edu (jose nazario)


while you didn't specify a platform, the first one that comes to mind
is hyperchem for the pc. we use it here to do just that, to calculate
water accessable surface areas with varying probe sizes. hyperchem can 
read in a pdb file and you can use it to select hydrophobic resiues and
from there calculate the ASA.

as for other platforms, there exist a plethora of such programs on UNIX
boxes. as far as macintosh and powermacs go, i am at a loss to provide
you with information as to what programs will fill your needs.

jose nazario

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


================================================================================

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/



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