Subject: Summary of replies: software for databases of chemical info

From: Irilenia Nobeli <[email-masked]>
Date: Tue, 8 Aug 2000 12:23:17 +0100 (BST)

Dear CCLers
I have received a wide range of responses to my question on software (free
and commercial) for databases of chemical structures. I was only going to
do a summary but I thought it best to let everybody read the original
answers so they can make up their own minds.

However, for those who don't want to go through the e-mails, and for what
it's worth, here is my conclusion (I must stress that we have not made a
decision yet as we are still waiting for quotations from a few companies).

 --- There does not seem to be any FREE software around that will allow
either the creation of a database of chemical structures (and of course
tools to retrieve data and do substructure/similarity searches) or an
interface to a standard relational database that will allow the handling
of chemical structures. If I am wrong about this one, please let me know!

 --- There are a few commercial products around that promise they can do
just the job. Most of them are guaranteed to set you back a few thousand
dollars, although allow me to praise ChemAxon for their policy regarding
the pricing of their product JChem. 
For a (hopefully near-complete) list:

   JChem from ChemAxon
   ISIS from MDL
   UNITY from Tripos
   MOE from the Chemical Computing Group
   RS3 from Oxford Molecular
   ACCORD from Synopsys
   ChemFolder from ACDlabs

(if I missed any, I'm sure someone will let me know!)

 --- I had recommendations (NOT FROM THE DEVELOPERS THEMSELVES!) for
JChem, RS3, ISIS and MOE. I would also like to point out that ChemFolder
cannot be interfaced to Oracle but its price is a fraction of most other
commercial software.

Finally, before I attach the original answers let me thank once again all
those who helped with their e-mails.

>From dark grey London,
       Irilenia

------------------------------------------------
Irene (Irilenia) Nobeli
Biomolecular Structure and Modelling Unit
Department of Biochemistry and Molecular Biology
University College London
Darwin Building
Gower Street
London
WC1E 6BT

[email-masked]
tel. 020 7679 2171
fax. 020 7679 7193

>>>  The greatest proof of the existence of
     intelligent life outside Earth is that
     they haven't contacted us yet.       <<<<

>>>>>>>>>>>>>>>>>>>> EDITED ANSWERS <<<<<<<<<<<<<<<<<<<<<<<<<

Date: Wed, 02 Aug 2000 14:47:27 +0100
From: Herbert Fruchtl <[email-masked]>

Hi Irilenia,

Knowing next to nothing about databases myself, here's a list of free
database applications for Linux:

http://metalab.unc.edu/pub/Linux/apps/database/!INDEX.html

I think the most widely used one is SQL, and in the www directory from
this page there's a CGI (that's a scripting language for web sites)
front-end. No idea if it's any good, or if it's useful for the type of
database you have in mind.

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Date: Wed, 2 Aug 2000 11:00:16 -0400 
From: Carlos Faerman <[email-masked]>

Irilenia,
There are two major players that utilize ORACLE to build such a database:
MDL and Oxford Molecular Group, UK. The former calls it ChemBio4Oracle
whereas the latter calls it RS3.
I am not aware of freeware to do this. You may also check Specs/BioSpecs in
Holland who have a Web interface that customers can use to purchase
compounds, naturally linked to their database which I believe is RS3-based.
Carlos

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Date: Wed, 2 Aug 2000 16:07:17 +0100
From: David S Coombes <[email-masked]>

[...]  I don't really have a reply to your
problem but if you want to have a web interface i think perl/cgi scripts can be
very useful.  What sort of information would your database contain?

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Date: Wed, 02 Aug 2000 11:29:11 -0400
From: "Michael K. Gilson" <[email-masked]>

Hi,

We are using JChem and are quite happy with it so far.

See "substructure search" in http://www.bindingdb.org

good luck,
Mike

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Date: Wed, 2 Aug 2000 16:36:00 +0100
From: Rob Williams <[email-masked]>

Hi,

Just for the record, you missed Oxford Molecular from your list
of commercial suppliers. We are the main suppliers of Oracle based
chemistry databases. We have had a product, RS3 (RS-cubed), on the
market for some years now that allows structures to be managed,
searched and retrieved directly in Oracle. It also supports combined
queries across chemical structure and any other data you might
have stored in Oracle. It is a full informatics solution with the
emphasis on information sharing between co-workers. We have a web
toolkit in final QA before release at the end of this month. This
allows you to put together your end web applications very quickly
using JavaServer Pages (JSP).

I mention this because if you do go for a commercial solution then
we really do have the best product offering. Other vendors may have
data cartridges for Oracle that can perform a substructure query but
RS3 is a full database application on top of this sort of technology.

You can get more information from our web site at http://www.oxmol.com,
and on the new web toolkit specifically at
http://www.oxmol.com/software/rs3iab.

Hope this is useful for you.
Best regards,
Rob

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Date: Wed, 2 Aug 2000 16:33:41 +0100 
From: "George, Ashley" <[email-masked]>

Hi,
I'm really interested in your note and the types of things you are trying to
do.

Is it possible to explain what you are finally going for? Substructure
searching, reaction searching, just text based searching?

Hopefully speak to yo usoon
Cheers
Ashley

Dr Ashley George
UK Group Leader Chemoinformatics
GlaxoWellcome Medicine Research Centre
Gunnels Wood Road
Stevenage
Hertfordshire
SG1 2NY UK

Direct Tel. +44(0)1438-764183   
Direct Fax. +44(0)1438-764918
email. [email-masked]

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Date: Wed, 02 Aug 2000 17:15:50 +0100
From: Mark Forster <[email-masked]>

Dear Irilenia

Mark here. I saw your question on the CCL, and thought I could add
my $0.02 worth. What is the hardware/OS on which you want to run
the database - is it exclusively SGI. For an alternative I would suggest
PostgresSQL or MySQL on a PC/Linux. I have Suse Linux 6.3 and these
are included in the box, although I dont have an application that uses
them (yet). The web interface would only need to be HTML/CGI/Perl
and the development effort here is quite low, there are also many examples
around.

[...]

Mark F

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Date: Thu, 3 Aug 2000 09:26:10 +1000
From: "Dr. Dave Winkler" <[email-masked]>
I would like to see a summary of responses please, Irilenia.

Cheers,

Dave

Dr. David A. Winkler                    Email: [email-masked]
Senior Principal Research Scientist     Voice: 61-3-9545-2477
CSIRO Molecular Science                 Fax:   61-3-9545-2446
Private Bag 10,Clayton South MDC 3169   http://www.csiro.au
Australia          

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Date: Wed, 02 Aug 2000 21:59:20 +0200
From: Thomas Strassner <[email-masked]>

Dear Irene,

though I can not give you any hints besides what you mentioned I would be 
very interested
in a summary of replies. Please post it to CCL, I think many people will be 
interested !!

Yours sincerely

Thomas Strassner

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Date: Thu, 03 Aug 2000 13:12:23 +0200
From: michael braunschweig <[email-masked]>

hi irilenia,

we tested the mdl database last year. the text as the structure search
are quite fast (if you have a server woth lot of memory - 4 *  rs64-ii
262 mhz  / 8mb L2 Cache, 6 bg memory). in my opinion the substructure
search is a very good feature.

michael braunschweig
department of chemistry
university of dortmund
germany

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Date: Thu, 3 Aug 2000 14:34:41 -0400
From: Gavin Shear <[email-masked]>

Dear Irilenia,

ACD/Chemfolder will suit your purpose. Please see www.acdlabs.com/downloads
for a free trial version.  Although the database is not currently Oracle
based,
academic prices are very reasonable, and multiple user database searching
etc. is supported.

Hope this helps,
Gavin Shear

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Date: Thu, 3 Aug 2000 17:59:06 -0400 (EDT)
From: Suzanne Sirois <[email-masked]>

Dear Irilenia,
        I have developed a software in JAVA that can access any database.
MS-ACCESS, MySQL, Oracle. What is important to know is what exactly you
want to do with the DB. Molecular Modeling, HTS, data mining, etc.

One software that has all of the above is MOE from Chemical Computing Group.
It is not free but much more cheaper than other commercial software.

Goud Luck,
Suzanne Sirois
Pharmaceutical Chemistry Business development officer

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Date: Fri, 04 Aug 2000 00:57:35 +0200
From: Ferenc Csizmadia <[email-masked]>

Hi Irilenia,

JChem suits your requirements:
- allows you to access, search and retrieve data,
- structures may be stored in Oracle (or other SQL-based relational
database system)
- supports web access
- used by academic institutions
- affordable
Since the software is in Java, you may use it under any OS-s (Linux,
Win32, Sun, SGI, ....)

Please check out http://www.jchem.com, where you can see the software
working (you can also download it for evaluation).

Regards,
Ferenc

--
Dr. Ferenc Csizmadia
ChemAxon Ltd.
http://www.chemaxon.com
T:+3620 9570988
mailto:[email-masked]

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Date: Fri, 04 Aug 2000 07:44:32 -0400
From: Anthony Arvanites <[email-masked]>

Dear Irilenia

Ferenc's software JChem would probably best fit your needs and its practically
free.  I highly recommend the JChem software.  If you decide to go with 
commercial
software, your best choice would be MDL.  MDL will give you a considerable
licensing discount because you are in a academic setting.  Good luck

Tony

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Date: Fri, 4 Aug 2000 09:59:12 -0400 (EDT)
From: Suzanne Sirois <[email-masked]>

Dear Irilenia,
        I have experience with MOE in the past and
what you are looking for is in it. Also, they have academic
price which are very good! Trust me it is a good program.

Please contact Bill Hayden at 514-393-1005
                           or 514 944 5953
                     [email-masked]

You can mention that I refer you to him.

Suzanne Sirois, Ph.D.
Pharmaceutical Chemistry business development officer
CERCA

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Date: Mon, 07 Aug 2000 14:02:55 EDT
From: Douglas Smith` <[email-masked]>

Irilenia:

You did not mention RS3 from Oxford Molecular in your mail to CCL.  It has 
been an Oracle technology for chemistry for far longer than any of the other 
commercial packages you mentioned.  If you would like, I will have a sales 
person call on you  or send you additional information about the product and 
academic pricing.

Doug Smith
Product Manager, Decision Support Software
OMG

[email-masked]
410-527-4571