From g-recht@chem.nwu.edu Fri Oct 31 11:42:12 1997 Received: from mercury.chem.nwu.edu for g-recht@chem.nwu.edu by www.ccl.net (8.8.3/950822.1) id KAA28530; Fri, 31 Oct 1997 10:36:50 -0500 (EST) Received: from nano (nano.chem.nwu.edu [129.105.14.190]) by mercury.chem.nwu.edu (8.8.5/8.8.5) with SMTP id JAA28166 for ; Fri, 31 Oct 1997 09:36:01 -0600 (CST) Message-Id: <3.0.3.32.19971031093934.0090b390@mercury.chem.nwu.edu> X-Sender: g-recht@mercury.chem.nwu.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Fri, 31 Oct 1997 09:39:34 -0600 To: chemistry@www.ccl.net From: "G. Rechtsteiner" Subject: Surface Area Summary Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" 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 merckel@mpibp-frankfurt.mpg.de 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: dorina@ks.uiuc.edu 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