Subject: Surface Area Summary

From: "G. Rechtsteiner" <[email-masked]>
Date: Fri, 31 Oct 1997 09:39:34 -0600

Thanks to everyone who responded to my question concerning
the solvent accessible surface area of proteins.  The responses
are summarized below.

Greg

1. 

Goto the EMBL website, they have the software for free.
www.embl-heidelberg.de/argos/ASC.21/asc2.html

Groeten, David.
________________________________________________________________________
Dr. Ir. David van der Spoel     Biomedical center, Dept. of Biochemistry
s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

2.

Here are some URLs I found helpful:
If you get other responses, I'd be very grateful for
a summary. Thanks.

http://hyper.stanford.edu/~mbg/ftp/SurfaceVolumes/
Get the source code archive near the bottom of the page.
It's a C package and compiles under linux without problem.

http://www.embl-heidelberg.de/~eisenhab/
Some more routines for surface/volume info.

http://csbmet.csb.yale.edu/people/core/pjf/pjf_hm.html
See ACCESS.

The CCP4 package has SURFACE and VOLUME utilities you may
look into them, but it'll be a bit of work getting the the
whole CCP4 suite up on linux just for those two.

http://sjh.bi.umist.ac.uk/naccess.html
This is a Fortran package. I had to contact the author
to get it to compile under linux (UniFix 2.0 Kernal2.0.18)

Michael
[email-masked]

3.

Consider the package MOLSV by Graham Smith (Calculation of Molecular
Volume and Surface Area), available from QCPE.  The QCPE reference number
is QCMP053, and can run on a PC. Have a good day.
Cherif Matta
Chemistry Dept.
McMaster University
Hamitlon, Ontario, Canada.

4.

The VMD program allows you to calculate and also display the
solvent accessible surface of any protein.
It's freely distributed and it's written in C++.

See http://www.ks.uiuc.edu/Research/VMD

Or you can use the Grasp program from Barry Honig's lab (I don't
know the URL for it) which, as far as I know, it's not free but is
not expensive either.

Good luck.
Dorina
---------------------------------------------------------
Theoretical Biophysics Group    Email: [email-masked]
Beckman Institute, UIUC         Phone: (217) 244-8946
405 North Mathews Ave.          Fax:   (217) 244-6078
Urbana, IL 61801, USA           http://www.ks.uiuc.edu/
---------------------------------------------------------

5.

   ICMlite is such a program. It will also let you display it,
calculate area by residue or by atom, plot the values etc.
ICMlite is free for academic institutions.
   Our site is http://www.molsoft.com
   Sincerely,

Rita,
Molsoft, LLC