From owner-chemistry@ccl.net Thu Mar 30 08:28:00 2006
From: "Marhoefer, R \(Richard\) Richard.Marhoefer^intervet.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Free software for drug design? ..and flexibility descriptors
Message-Id: <-31366-060329123519-11463-Wj2ykyNMMpuF02CQVNH1yA]*[server.ccl.net>
X-Original-From: "Marhoefer, R \(Richard\)" <Richard.Marhoefer ~~ intervet.com>
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Date: Wed, 29 Mar 2006 18:49:18 +0200
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Sent to CCL by: "Marhoefer, R \(Richard\)" [Richard.Marhoefer_+_intervet.com]

Dear Marc,

a number of free programs and/or open source programs for some of the desired application areas are listed in:

J.W. Geldenhuys, K.E. Gaasch, M. Watson, D. Allen, C.J. van der Schyf (2006) Optimizing the use of open-source software applications in drug discovery. DDT 11, 127-132.

Richard

________________________________
Dr. Richard J. Marhöfer
BioChemInformatics Scientist
Intervet Innovation GmbH
Drug Discovery / BioChemInformatics
Zur Propstei, 55270 Schwabenheim, Germany
E-mail: richard.marhoefer(~)intervet.com
Phone: +49 6130 948-204
Fax:     +49 6130 948-517
Intervet is an Akzo Nobel Company



> -----Original Message-----
> From: owner-chemistry(~)ccl.net [mailto:owner-chemistry(~)ccl.net] 
> Sent: Montag, 27. März 2006 12:15
> To: Marhoefer, R (Richard)
> Subject: CCL: Free software for drug design? ..and 
> flexibility descriptors
> 
> 
> Sent to CCL by: Marc Baaden [baaden%x%smplinux.de]
> 
> Dear All,
> 
> concerning techniques like molecular dynamics, Monte Carlo or 
> implementations of ab initio approaches there are a number of 
> freely available programs for the academic community. I 
> wonder whether similar 'free' (non-commercial) software 
> exists for drug design? In particular for the following tasks:
> - virtual screening
> - pharmacophore modeling
> - receptor mapping
> - QSAR and 3D-QSAR
> - Shape alignments
> - ComFa-like methods
> My focus would be more on exploring these approaches then on 
> applying them in a production environment on huge projects. 
> I'd be very grateful for suggestions and comments.
> 
> One more specific request: what type of molecular or atomic 
> descriptors do exist for conformational flexibility?
> 
> Thank you very much in advance,
>   Marc Baaden
> 
> -- 
>  Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>  mailto:baaden|a|smplinux.de      -      http://www.baaden.ibpc.fr
>  FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217
> 
> 
> 
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