clogP summary
Netters,
five days ago I asked the following question;
> are there some kind of programs available to calculate logP, delta logP,
> solvation values preferably on PC or Mac available to an affordable price.
>
I'd like to thank all of you who answered my request and post the summary
to the net.
Pierre
*****************************************************************************
Summary
******************************************************************************
Hi -
There was a similar question a while ago - I still
have the summary. I'll mail it on to you and hope
it is useful.
Best wishes
David
David E. Clark |
Proteus Molecular Design Ltd., | Tel: 01625-500555
Lyme Green Business Park, | Fax: 01625-500666
Macclesfield, Cheshire, | Email: D.E.Clark' at \`proteus.co.uk
SK11 0JL, UK |
Date: Fri, 26 Aug 94 09:47:47 EST
From: pballester <pballester' at \`cubist.com>
Hello,
Thanks to everybody who responded to my question regarding logP calculation
software.
Here i is a summary of replies I got to my question.
****************************ANSWERS******************************************
>From riusal' at \`redvax1.dgsca.unam.mx Thu Aug 25 22:51:09 1994
I have used Hyperchem and chemplus to do LogP calculation of organic
compounds and the agreement is quite good. Chemplus is a program that
runs under Hyperchem Autodesk use to market Hyperchem but now is market
directly from Hypercube from Canada.
With my best regars
Carlos
============================================================
>From dec' at \`proteus.co.uk Fri Aug 26 07:39:56 1994
Dear Pau
I'm not sure if there is a corresponding program available but there
was recently a good article on the subject :
' at \`article{Klop94 ,
author = "Klopman, G., Li, J.-Y., Wang, S. and Dimayuga, M. ",
title = "Computer Automated log P Calculations Based on an Extended Group
Contr
ibution Approach ",
journal = "Journal of Chemical Information and Computer Sciences ",
year = "1994 ",
volume = "34 ",
pages = "752--781 ",
}
Best wishes
David E. Clark
=============================================================
Hello Pau,
A good commercial PC program for calculating log P is available from
CheMicro Ltd
Hegedus Gy. u. 6.
H-1136 Budapest
Hungary
phone: (+36-1)-131 3847
fax: (+36-1)-132 9330
best wishes
Tamas
*****************************************************************************
Tamas E. Gunda phone: (+36-52) 316666 ext 2479
Research Group of Antibiotics fax : (+36-52) 310936
L. Kossuth University e-mail: tamasgunda' at \`tigris.klte.hu
POBox 36 tamasgunda' at
\`huklte51.bitnet
H-4010 Debrecen
Hungary
*****************************************************************************
=============================================================
>From HODGKINE' at \`prince.mm.wyeth.com Fri Aug 26 03:14:48 1994
From: Hodgkin, Ed
Date: Fri, Aug 26, 1994 8:43 AM
Subject: LogP
To: pau' at \`cubist.com
Pau
I'm also interested in logP calculation. Can you post a summary of replies to
the CCL please?
Edward Hodgkin
Wyeth Research (UK) Ltd
hodgkine' at \`prince.mm.wyeth.com
=============================================================
Hello Pau,
A good commercial PC program for calculating log P is available from
CheMicro Ltd
Hegedus Gy. u. 6.
H-1136 Budapest
Hungary
phone: (+36-1)-131 3847
fax: (+36-1)-132 9330
best wishes
Tamas
*****************************************************************************
Tamas E. Gunda phone: (+36-52) 316666 ext 2479
Research Group of Antibiotics fax : (+36-52) 310936
L. Kossuth University e-mail: tamasgunda' at \`tigris.klte.hu
POBox 36 tamasgunda' at
\`huklte51.bitnet
H-4010 Debrecen
Hungary
*****************************************************************************
=============================================================
Dear Dr. Ballester;
CompuDrug Chemistry, Ltd. markets a pretty good Windows-based programme
called "PrologP 5.0" which enables you to estimate log P values for
organic
molecules from input structural information. For more information, contact:
Dr. Zoltan Bencz, Marketing Director
CompuDrug Chemistry, Ltd.
Fuerst Sandor utca 5
H-1136 Budapest, Hungary
Internet: bz' at \`cdk-cgx.hu or mktg' at \`cdk-cgx.hu
FAX-nr: (0036 1) 132-2574
Dr. Bencz is most helpful and fluent in English. Needless to say, PrologP
5.0 is also in English. The programme is relatively simple and straightfor-
ward, doesn't require VAX or other expensive, high-power computers/work sta-
tions, and you can learn how to use it rather quickly without the assistance
of a couple of Ph.D. computational chemists standing behind you. What more
can you ask for?
Best regards,
(Dr.) S. Shapiro
Institute fuer orale Mikrobiologie und allgemeine Immunologie
Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich
Plattenstrasse 11
Postfach
CH-8028 Zuerich, Switzerland
Internet: toukie' at \`zui.unizh.ch
FAX-nr: (0041 1) 261'56'83
=============================================================
Try CHEMICALC-2 from QCPE. Available in PC and VAX (?) versions
Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design
Research Division
e-mail: bowlus' at \`sandoz.com Sandoz Agro, Inc.
Phone: + 1 415 354 3904 975 California Ave.
Fax: + 1 415 857 1125 Palo Alto, CA 94304
=============================================================
>From riusal' at \`redvax1.dgsca.unam.mx Thu Aug 25 22:51:09 1994
I have used Hyperchem and chemplus to do LogP calculation of organic
compounds and the agreement is quite good. Chemplus is a program that
runs under Hyperchem Autodesk use to market Hyperchem but now is market
directly from Hypercube from Canada.
With my best regars
Carlos
=============================================================
> Does anybody know of some program or utility to calculate logP
> values for organic compounds. Please E-mail directly to me.
>
I sell a program called MOLGEN which calculates log(p), also,
distribution on surface or in a plane of the molecule. The latter
calculation is displayable/plottable as a color gradient depiction. It
can also calculate conformationally/temperature dependency with respect
to log(p). Henry's constant is being added shortly.
The program is also a full-featured 3-D modelling program and database
with MM2, etc. There is a demo on ccl.net in
/pub/chemistry/software/MS-DOS/MOLGEN-demo. Please let me know if I can
be of further assistance.
PS: I have also used LOGKOW from Syracuse Research, an excellent
program, but lacks the feature set in Molgen.
Eric
_____________________________________________________________________
J. Eric Slone Scientific Consulting Services
Serving Government & Industry Since
1982
Internet: eslone' at \`mason1.gmu.edu
Compuserve: 73757,2776 "True science teaches, above all, to
Fax: (703) 751-6639 doubt, and to be ignorant."
Voice: (703) 461-7078 Miguel do Unamuno
______________________________________________________________________
=============================================================
>From shaomeng' at \`helix.nih.gov Thu Aug 25 16:37:32 1994
Dear Pau,
We have developed a logP calculation model and the paper concering it
has been published in Journal of Chemical Information and Computer Sciences,
1994, Vol. 34, pages 752. I will be gald to send you a reprint if you need.
If you are also interested in the program, you can get in touch with
Dr. Mario Dimayuga at Case Western Reserve Univ (216)368-3699. I am sure
he will be happy to anwser your questions.
Hope this will help.
With my best regards,
-- Ju-Yun Li ---
Department of Chemistry
Case Western Reserve University
Cleveland, Ohio 44106
===========================================================
Computational Chemistry Scientists:
I have seen a number of queries on this forum about hydrophobicity. A new
program to evaluate HYDROPHOBICITY at the atomistic level recently became
available, called HINT. Thanks to Tudor-Ionel Oprea for support comments of
HINT. This program is based on empirical data and hydrophobic fragment
work of Hansch, Leo, Abraham, and Kellogg. The program can: calculate log P
(of small molecules and proteins), score ligand/macromolecule and
macromolecule/macromolecule interactions, calculate 3D HYDROPATHY
(hydrophobic + hydrophilic) fields, create hydropathic complementarity
maps, produce unique 3D hydropathic interaction maps, and is interfaced
with InsightII, Sybyl and ChemX. If you are interested in additional
information or a free trial of this software, please see the file
HINT.note on the CCL archivess (infomeister) or contact me at the address
below.
You can find a comprehensive list of HINT functionality, the references
to publications which describe HINT use, and ordering information in
CCL archives. To get it via mail, send a message:
select chemistry
get info/software-packages/HINT.note
to MAILSERV' at \`ccl.net. This file is also available via gopher/anon.ftp/WWW
from
the /pub/chemistry/info/software-packages/HINT.note on www.ccl.net:
gopher www.ccl.net 73 (info/software-packages/Hint.note)
--
************** David N. Haney, Ph.D. ****************
* Haney Associates Phone - 619-566-1127 *
* 12010 Medoc Ln. *
* San Diego, CA 92131 Fax - 619-586-1481 *
************** Email - haney' at \`netcom.com ***************
============================================================
A public domain program for calculating logP of small molecules is
CHEMICALC-2, available from QCPE for VAX or PC (QCPE 608 or QCMP 129,
respectively).
Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design
Research Division
e-mail: bowlus' at \`sandoz.com Sandoz Agro, Inc.
Phone: + 1 415 354 3904 975 California Ave.
Fax: + 1 415 857 1125 Palo Alto, CA 94304
==============================================================
Thanks again,
Pau
Pablo Ballester
Cubist Pharmaceuticals, Inc.
24 Emily St.
Cambridge MA 02139
E-mail: pau' at \`cubist.com
David E. Clark |
Proteus Molecular Design Ltd., | Tel: 01625-500555
Lyme Green Business Park, | Fax: 01625-500666
Macclesfield, Cheshire, | Email: D.E.Clark' at \`proteus.co.uk
SK11 0JL, UK |
Pierre,
Spartan is able to calculate LogP's - there is one model in V3.1 and
two additional models in V4.0 (which is due to ship in April). Have you seen
or used Spartan - I recall that Ciba in the US is running the code... Several
models (Bodor, Ghose/Crippen, Villar) have been described in the literature in
the last couple of years (J Am Chem Soc and J Comp Chem).
Joe
--
------------------------------------------------------------------------
Joe Leonard
Wavefunction Inc.
18401 Von Karman, Suite 370
Irvine, CA 92715 I am a professional...
714-955-2120 do not attempt this at home.
714-955-2118 fax
jle' at \`wavefun.com
Hi, Pierre.
> are there some kind of programs available to calculate logP, delta logP,
> solvation values preferably on PC or Mac available to an affordable price.
The QSAR Properties module of our ChemPlus package will calculate logP,
hydration energy, and a variety of other properties. We do not have a
version for the Mac; our software runs under Windows on a PC. This
ChemPlus module works only with our own .HIN format; to get much use out
of the program you would need to use HyperChem. I can send you information
about both of these programs if you wish. The academic price for HyperChem
is $US995, and for ChemPlus, US$495.
Regards,
Joel
------------
Joel Polowin, Ph.D. Manager, Scientific Support
Email to: polowin' at \`hyper.com
Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
Info requests to: info' at \`hyper.com Support questions to: support' at
\`hyper.com
Email group: Send "subscribe hyperchem" to hyperchem-request' at
\`hyper.com
I would appreciate it very much if you would forward to me any replies you
recieve on this.
The CaCHe system includes a program called BlogP by N. Bodor which will
calculate logP, with some restrictions after a MOPAC calculation has been
performed.
Personal Cache is software which will run on a MAC (though I'm not sure it
includes MOPAC). Otherwise you will need a server/card for your system.
It is very user friendly.
*******************************************************************************
Randy Winchester
Institute for Drug Development
14960 Omicron Drive
San Antonio TX 78210
(210) 677-3800 ph
(210) 677-8814 fax
rwinches' at \`arnie.iddw.saci.org
*******************************************************************************
> are there some kind of programs available to calculate logP, delta logP,
>solvation values preferably on PC or Mac available to an affordable price.
I would like to see the summary of the responses you receive to this query.
Thank you.
Wally
========================================================================
Walter E. Reiher III, Ph.D. WallyR' at \`netcom.com
Consultant in Computational Chemistry
P.O. Box 61056 voice 408-720-0240
Sunnyvale, CA 94088 fax 408-720-0378
Hello,
BioByte offers a Mac version of Al Leo's cLogP (Chem. Rev.
1993, 93, 1281). I believe the academic price is approximately
$400. You can reach BioByte at P.O. Box 517, Claremont, CA 91711.
Email: clogp' at \`medchem.claremont.edu or WWW http://medchem.claremont.
edu.
Nancy Brichford
Monsanto
New Ag Products
St. Louis, MO
nlbric' at \`mtcamm.monsanto.com
Im sure others will inform you, but Al Leo's group at Pomona (BioByte),
is offering the clogp program for mac, and soon to offer a pc version.
(email al' at \`iris.claremont.edu). You might also see Meylan & Howard,
Atom/Fragment contribution method for estimating octanol-water
partition coeffs", J Pharm Sci, 1995, 84, 83-92 - program LOGKOW.
>From: "Dr.Pierre Acklin" <acklin' at \`chbs.CIBA.COM>
>Date: Fri, 31 Mar 1995 14:45:34 +0000
>Subject: CCL:calculated logP
>
>Dear Netters,
>
> are there some kind of programs available to calculate logP, delta logP,
>solvation values preferably on PC or Mac available to an affordable price.
>
>Pierre
Dear Dr. Acklin:
We (BioByte Corp., based in Claremont, CA) have a ClogP calculator
available for the Macintosh, called MacLogP. It uses the same fragment
based methodology as our Medchem ClogP for the VAX, developed by Drs.
Albert Leo and Corwin Hansch. It accepts SMILES input in single and
batch mode, and output can be given in three levels of verbosity:
terse, detailed, and verbose. A 2D depiction is also given to verify
structure. In addition to the ability to calculate ClogP, it also
contains high confidence measured values for 9000 well-known
structures, which can also be searched for by name.
We can send you a copy with a 30 day evaluation license either on a
diskette or via e-mail. For the e-mail version, you would need to be
able to decode BinHex4.0 (.hqx) files. If, after evaluating the
program, you should wish to purchase it, we can send you a permanent
license for $998. Please e-mail me and let me know if you would like us
to send you the evaluation copy, and which method of delivery you would
prefer.
Looking forward to hearing from you,
Michael L. Medlin
BioByte License Manager
--
michael l. medlin | biobyte
al' at \`iris.claremont.edu | phone 909.624.5992
http://iris.claremont.edu/~al/ | fax 909.624.1398
Subject: Time:10:44 AM
OFFICE MEMO LOG P Date:3/31/95
MacClogP is a Macintosh version of the well known CLOGP program. MacClogP
is available from Biobyte Corp at the following address:
Biobyte Corp.
201 West 4th St. Suite 204
Claremont, CA 91711
USA
Phone: 909-624-5992
FAX: 909-624-1398
Email: biobyte' at \`medchem.claremont.edu
Gene
Pierre:
There is a code, HINT, which adds onto the Sybyl, InsightII or ChemX
molecular modeling interface. This code not only calculates logP but
creates 3-D hydropathy fields to assist in understanding docking. HINT
is available for SGI only and the commercial price for one machine is
$5,000. Should you be interested in trialing this software for free,
I will send you a demo license.
--
************** David N. Haney, Ph.D. ****************
* Haney Associates Phone - 619-566-1127 *
* 12010 Medoc Ln. *
* San Diego, CA 92131 Fax - 619-586-1481 *
************** Email - haney' at \`netcom.com ***************
Dear Pierre,
I am not very familiar with those kinds of calculations, but I think
the programs you are looking for are a part of the CAChe Worksystem.
CAChe Europe can be reached at:
Alan Day
European Sales Manager
tel (0628) 486000
fax (o628) 474799
in England.
Hope this is of any help.
Best regards,
Mirko Kranenburg
University of Amsterdam
Dept. of Inorganic Chemistry and Homogeneous Catalysis
Nieuwe Achtergracht 166
1018 WV Amsterdam
The Netherlands
tel. +31-20-5256417
fax. +31-20-5256456
e-mail: mirko' at \`sara.nl
Hi Pierre,
These are the responses I got for similar question I asked to
the net several months ago. You are welcome to use them.
I have edited some of them in the sake of space.
Cheers,
Ramon
__________________________________________________________________________
It depends on what you want to do with the logP value. The CompuDrug and
Daylight Chemical Information (MedChem) software vare both fairly expensive. A
good inexpensive (US$200) option is the Hint! program of Abraham and Kellogg
(Virginia Commonwealth University). Glen Kellogg can be reached by email
(gkellogg' at \`gems.vcu.edu). It can also plot lipophilicity contours around
molecules and can create lipophilic fields for use in CoMFA.
Cheers,
Dave
Dr. David A. Winkler Voice: 61-3-542-2244
Principal Research Scientist Fax: 61-3-543-8160
CSIRO Division of Chemicals and Polymers
Private Bag 10
Clayton, Australia.
__________________________________________________________________________
I have been interested in the log(P) calculators but also have had
difficulty getting information. Also, I'm not sure how accurate they are.
When I need to calculate a log(P), I usually do it "by hand" from the
data
provided by Rekker in his "Hydrophobic Fragmental Constant" work. I
am
well versed in the method and find it generally gives good answers. We
have published a couple of papers with this approach. I'll give you the
references in case they might be useful to you:
"Development of Hydrophobicity Parameters to Analyze Proteins Which
Bear Post- or Cotranslational Modifications", Black, S.D., and
Mould, D.R. (1991) Anal. Biochem. 193, 72-82.
"Development of Hydrophobicity Parameters for Prenylated
Proteins",
Black, S.D. (1992) Biochem. Biophys. Res. Commun. 186, 1437-1442.
Cheers,
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
= Shaun D. Black, PhD | Internet: shaun%jason.decnet' at \`relay.the.net
=
= Dept. of Biochemistry | University of Texas Health Center, at Tyler =
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
__________________________________________________________________________
One package for calculating LogP is Polaris from Molecular Simulations
Inc. This program employs the protein dipole-Langevin dipole method of
Arieh Warshel. This method has been successful in calculating free energies
of solvation, free energies of binding, delta pKa, and LogP values.
Nick Reynolds
Molecular Simulations Inc.
16 New England Executive Park
Burlington, MA 01803-5297 USA
1-617-229-9800
__________________________________________________________________________
You can reach compudrug sales person Harlod Borgsted at (716) 292-6830.
I think that this is a New York number.
By the way, we have the ProLogP software and would like to comment on a few
items.
First, It may be limited in that some compounds containing unique fragments
will not compute with this software. The method is a fragment addition
method where it splits your compound into parts that it has in it's datbase
and then adds up the LogP values.
Also, Charged compounds and some particular ringsystems cannot be used.
And most importantly, isomers are given the same LogP values. Example-
move a hudroxyl para, ortho or meta on an aromatic group. The log P will
be the same!
Or move a hydroxyl around a steroid ring, all will have the same LogP.
We compaired to the Daylight Chemical LogP stuff (much more expensive) and
found similar limitations. The values were not the same (even close to
each other) between the packages).
So. for use in QSAR, we do not use either of these.
We have found a LogP method that works from the atom level rather than the
fragment level and have used it to some extent. It handles all compounds
but still has the isomer problem.
Contact: Arup K. Ghose at Sterling Winthrop Research group, 81Columbia
Turnpike, Rensselaer, NY, 12124 phone: (215) 983-5499
Ref is: J. Med. Chem. 1991, around Jan 17 or so. (sorry I don't have exactly)
He developed the software and should give you a copy if you send a tape.
Contact him first to set up arrangement.
Good luck,
Tom
PS
see the Hansch paper of a few months ago to review usefullness of logP.
Debnath, A. K.; Hansch, C.; Kim, K. H.; Martin, Y. C. Mechanistic
interpretation of the genotoxicity of nitrofurans (antibacterial agents)
using quantitative structure-activity relationships and comparative
molecular field analysis. Journal of Medicinal Chemistry. 1993 Apr 16;
36(8): 1007-1016.
##################################################
Tom Wiese
Department of Biochemistry
Wayne State University School of Medicine
540 E. Canfield
Detroit, MI
48201
Phone: (313) 577-5605
FAX: (313) 577-2765
email: tom' at \`sgih.roc.wayne.edu
##################################################
--
--
____________________________________________________________________
Dr. Pierre Acklin email: acklin' at \`chbs.ciba.com
smail: Ciba-Geigy AG tel: ++41 61 696 23 62
K-136.P.69 tel: ++41 61 696 23 75
CH-4002 Basel fax: ++41 61 696 27 61
_____________________________________________________________________