Subject: Summary: software for calculating solvent-accessible areas

From: Shcherbukhin Vladimir <[email-masked]>
Date: Mon, 10 Jun 1996 14:58:19 +0200

Hi folks,

Many many thanks to everybody who has replied to the question which I
recently posted on behalf of my colleague Marcel Linschoten. Some of you
were interested in getting summary of replies, so here it is.

Best regards,

Vlad

 ---------------------------------------------------------
Vladimir Scherbuhin  (Ph.D.) ! phone:  (+46-31)-776-2560
Precl. R&D, ASTRA Hassle AB  ! FAX:     (+46-31)-776-3710
Molndal S-43183, SWEDEN  !
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internet: [email-masked]
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========================================================
>Hello folks,

>I'm looking for a program (may also include Sybyl SPL) to calculate
>hydrophobic and hydrophilic areas on the solvent accessible surface of a
>small
>molecule. Who can help ?

>Thanks,

>Marcel Linschoten, Sweden

========================================================
Marcel:

You might try HINT as it interfaces with Sybyl.  It's available from
EDUSOFT.  See their web page for details:

http://www.eslc.vabiotech.com/

 ---------------------------------------------------------
J. Bruce Pitner, Ph.D.                 [email-masked]
Becton Dickinson Research Center           (919) 990-2147
P.O. Box 12016, RTP, NC 27709          Fax (919) 549-7572
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=========================================================
Hi,
There is a program writen by P. Gaillard for Sybyl who calculate MLP and
log P his name is Clip1.1.
We are using it at the university of Namur and it seems it works well. If
you are interested by thie program contact  me.
best regards,
fred Ooms

 ---------------------------------------
Ooms Frederic
Faculte Universitaire Notre-Dame de la Paix
Laboratoire de Chimie Moleculaire Structurale
Rue de Bruxelles 61
B-5000 Namur (BELGIUM)
Tel : 32(81) 724569 - Fax : 32(81) 724530
e-mail :[email-masked]
=========================================================
Hi

Under SYBYL the best program to do that is an option Call Molcad. This
program is able to display molecular properties on Connolly surfaces and
Electron density surfaces.

The only problem is that you need an SGI with 24 bitplanes and hardware Z
bufferinstall. It is working well with an R4000 Indigo Elan

Bye

 --
_____________________________________________________________________
___________

Jacques-Antoine DURET              GROUPE DE PHARMACOCHIMIE
MOLECULAIRE
UFR DE PHARMACIE              Universite Joseph Fourier
GRENOBLE
5 Avenue de Verdun            Tel : (33) 76 04 10 00
38243 Meylan FRANCE           Fax ; (33) 76 41 85 71
          E-Mail : [email-masked]
_____________________________________________________________________
=========================================================
SAVOL2 is what you are looking for. I got it from Bob Pearlman at University 

of
Texas, but it might be included with Sybyl.

[email-masked].

Yvonne Martin
Abbott Laboratories
=========================================================

Created, developed and extensively tested at the Institute of
Medicinal Chemistry of the University of Lausanne , CLIP is
a package with the following capabilities:

Computation and representation of the Molecular Lipophilicity Potential
(MLP)
on the solvent-accessible surface of molecules and macromolecules;
Calculation of n-octanol/water partition coefficients (log Poct) from the 
MLP
on the solvent-accessible surface;
Calculation of virtual log P values for individual conformers, and 
exploration
of the lipophilicity range accessible to a compound;
Computation and representation of the MLP in a given region of space
around molecules and macromolecules;
Computation and incorporation of the MLP into Comparative Molecular
Field Analysis (CoMFA)?.

Information about CLIP, publications can be found on the web at:

                                        http://www.unil.ch/pharm/clip/

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

Frederic Billois
Universite de Lausanne
Section de Pharmacie.
Institut de Chimie Therapeutique.
CH-1015 Dorigny-Lausanne
Suisse

Tel  : +41.21.692.45.24
Fax : +41.21.692.45.05
e-mail  : [email-masked]
WWW : http://www.unil.ch/pharm/ict/docs/ict.html

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=========================================================
Dear Marcel:

     I have written an SPL script to calculate surface areas using the SAVOL
program that is shipped with Sybyl 6.2.  The script will also calculate per
residue and per static set contributions to the surface area.  If you define
two statics sets, one for hydrophobic and another for hydrophilic atoms, my
script should calculate exactly the quantities that you are interested in.

    The next e-mail message contains a copy of my SPL script.  I hope you 
find
it useful.

    Ciao,

Konrad

 ------------------------------------------------------------------
| Konrad Koehler              |  Computational Chemistry Group     |
| internet:  [email-masked]  |  Department of Medicinal Chemistry |
|                             |  IRBM                              |
| telephone: +39-6-910-93606  |  Via Pontina Km. 30,600            |
| fax:       +39-6-910-93225  |  00040 Pomezia (Roma)              |
|                             |  Italy                             |
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=========================================================

Note: those of you who would like to get the SPL script, please send a
message directly to Konrad Koehler.