Subject: Re: CCL:distributed pharmacophore searching

From: "Osman F. Guner" <[email-masked]>
Date: Mon, 09 Apr 2001 08:47:40 -0500

It really depends on what exactly you mean with "pharmacophore."  The 
concept has been used differently by different people.

For example, some medicinal chemists equate Pharmacophore with a common 
scaffold among a given set of molecules.  For this, several algorithms such 
as maximum common sub-graph approach are available.

If you mean alignment of a given set of molecules, there are many alignment 
programs available (e.g., that will minimize the RMS for a given set of 
atoms, or maximize the overlap of steric and/or electrostatic fields).  Of 
course, more relevant ones involve overlap of common chemical features (as 
opposed to topological features) such as HBond donor/acceptor.

Pharmacophores from receptor active sites require more sophisticated 
programs and there are very few available.

Finally, looking at the wording of your question, you may be simply wanting 
a 3D-database searching program.

At any rate, I don't know if any of the above are available in Linux 
clusters today... would be interested to hear what you find out.

At 12:28 AM 4/9/01, Kim Branson wrote:

>Hi CCLers
>
>I'm looking for a program that is able to query a database(s) of small
>molecules for compounds that have characteristics of a pharmacophore. I
>know things like unity exist and that sort of functionality would be
>useful, however i plan to run such code on a linuc based beowulf cluster.
>Has anyone heard of/used any tools for a such a purpose and found them
>useful?
>
>regards
>
>Kim Branson
>
>______________________________________________________________________
>
>Mr Kim Branson
>Phd Student
>Structural Biology
>Walter and Eliza Hall Institute
>Royal Parade, Parkville, Melbourne, Victoria
>Ph 61 03 9662 7136
>Email [email-masked]
>
>______________________________________________________________________
>
>
>
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---
Osman F. Güner, Ph.D.
Director,  Lead Identification & Optimization
Molecular Simulations Inc.   (858) 799-5341
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