Subject: Summary cavities in protein-ligand complexes

From: Knegtel Ronald <[email-masked]>
Date: Mon, 31 Aug 1998 11:10:30 +0200 (WDT)

Dear all,

below follows a summary of the replies I received on my question about
measuring cavities in protein-ligand complexes. Thanks to everybody
for sending me information!

Ronald Knegtel

------------------------------------------------------------------------
You might look at Craig Taverner's steric program
(ftp://hobbes.gh.wits.ac.za/pub/steric/) based on solid angles.  The
solid angle corresponds to a projection onto an enclosing sphere.  The
program also has the complementary ability to measure cavities (like
those in zeolites).  It will also calculate the molecular volume and
radial extent, so from that, the solid angle data and the volume of a
sphere, you can probably calculate just about anything you're looking
for.

> - Jack
> 
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>  Jack A. Smith             ||
>  Union Carbide             || Phone:  (304) 747-5797
>  Catalyst Skill Center     || FAX:    (304) 747-4672
>  P.O. Box 8361             || 
>  S. Charleston, WV  25303  || [email-masked]
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-

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

Hi Ronald,
SURFNET from Janet Thornton's group will do what you want.  It's
available at:

http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html
Cheers
Michael
-- 
#################################################################
Dr Michael Dooley 
Centre for Drug Design and Development
The University of Queensland St Lucia, Qld, 4072 Australia
Brisbane Molecular Modeling Group http://www.uq.edu.au/~ddmdoole/

----------------------------------------------------------------------------
Hi,

	The grasp package calculates volumes/surfaces of molecules and also
cavities. All the functions are available through a graphical
interface(http://honiglab.cpmc.columbia.edu/). Another interesting
package is O. One of the programs (VOIDOO) calculates 3 different
cavities (probe acccessible, probe center accessible and Van der Waals )
(http://alpha2.bmc.uu.se/~alwyn/).
-- 

				WURTZ Jean-Marie

________________________________________________________________________
IGBMC               			E-mail : [email-masked] 
Laboratoire de Biologie Structurale	Phone :  (33) 3 88 65 35 29
Parc d'Innovation			Fax :	 (33) 3 88 65 32 01
1, rue Laurent Fries, BP 163
67404 ILLKIRCH, CU STRASBOURG
France    
________________________________________________________________________

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

Try VOIDOO from Uppsala Software Factory.

http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html

Mirek

*******************************************************************************
  
        Jaromir MAREK                  e-mail:[email-masked]          
                                       tel. ++ 420-5-411-29-411
                                       fax. ++ 420-5-412-11-214  
    X-ray Laboratory of
Dept. of Inorganic Chemistry           http://www.sci.muni.cz/~dusan/inorg.html
              &                          
Laboratory of Biomolecular             http://www.chemi.muni.cz/lbsd/lbsd.html
 Structure and Dynamics                
                                         
  Faculty of Science                   http://www.sci.muni.cz/
  Masaryk University                   http://www.muni.cz/
  Kotlarska (street) 2                 
  BRNO                                 
  CZ 611 37                            
  Czech Republic                          
-----------------------------------------------------------------------------

>From [email-masked]  Tue Aug 25 18:23:14 1998

Greetings,

Two software packages you might be most interested in:

Surfnet:

http://bsmcha1.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html

MSRoll

http://www.biohedron.com/msp.html

Hope this helps,

Cory Bystrom

---------------------------------------------------------------------------
>From [email-masked]  Tue Aug 25 18:00:43 1998

Dear Ronald,

you could try surfnet 
http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
that comes free for academic users (as far as i remember) or,

icm, 
http://www.molsoft.com

a (very good) commercial solution for your problem.

best Regards,
Fuad
Fuad Abdallah
Max-Planck-Institut fuer Zuechtungsforschung / ZWDV
Tel.: 0221/5062-739 / Priv: 0221/584563
--------------------------------------------------------------

>From [email-masked]  Tue Aug 25 17:22:34 1998

Hi !

I'm not sure exactly what kind of cavity you're talking about,
but if it is defined through a polygonal surface, the marching
cube algorithm will give you both surface and volume. The original
article is Lorensen & Cline, Comp. Graph., vol.21, no. 4, '87, p163

bye, Martin.

-------------------------------------------------------------------------------
Dr. Ronald M. A. Knegtel                     Research Scientist
Dept. of Molecular Design and Informatics    Phone  : +31-412-661469
N.V. Organon, RK2340                         Fax    : +31-412-662539
P.O. Box 20  5340 BH Oss                     http://www.organon.com/
The Netherlands                     E-Mail : [email-masked]
-------------------------------------------------------------------------------