From owner-chemistry@ccl.net Mon Mar 27 06:59:00 2006 From: "Alex Allardyce aa%x%chemaxon.hu" To: CCL Subject: CCL: Free software for drug design? ..and flexibility descriptors Message-Id: <-31334-060327065714-32471-uW8tJsodiG5mKwm9lWnHFA .. server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------080901090202000804040304" Date: Mon, 27 Mar 2006 13:01:00 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa!A!chemaxon.hu] This is a multi-part message in MIME format. --------------080901090202000804040304 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit HI Marc, ChemAxon have a range of products for core cheminformatics and drug discovery. We made all products free for academic teaching and research. You can find out more here about the conditions here (http://www.chemaxon.hu/forum/ftopic193.html). I list below the main tool classes Hope it's useful Cheers / Alex *ChemAxon toolkits* currently available * *Marvin *for editing and viewing chemical structures, reactions and queries; http://www.chemaxon.com/marvin/ * *Calculator Plugins* for prediction of various properties based on structure; http://www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins.html * *JChem Base* for structure and reaction searching and database handling; http://www.jchem.com/ * *JChem Cartridge* for Oracle® database integration; http://www.chemaxon.com/jchem/doc/guide/cartridge/index.html * *Standardizer* for structure canonisationhttp://www.jchem.com/index.html?content=doc/user/Standardizer.html * *Reactor *for structure transformations and library enumeration; http://www.jchem.com/index.html?content=doc/user/Reactor.html * *Screen *for pharmacophore and structure based screening; http://www.jchem.com/index.html?content=doc/user/Screen.html * *JKlustor* for clustering and diversity analysis; http://www.jchem.com/index.html?content=doc/user/JKlustor.html * *Fragmenter *for decomposition to fragments and r-groups; http://www.jchem.com/index.html?content=doc/user/Fragmenter.html *Implementations on our website *(Java required)*:* Marvin and Calculator Plugin (unlimited structure based predictions for pKa, logP, logD, polar surface area (PSA), charge distribution, polarizability prediction, H-bond aceptor/donor, tautomer, resonance, major microspecies, reactivity, refractivity and elemental analysis) :http://www.chemaxon.com/demosite/marvin/index.html MarvinSpace: http://www.chemaxon.com/shared/MarvinSpace/index.html JChem: http://www.jchem.com/index.html?content=examples.html Reactor: http://www.jchem.com/examples/reactor/jsp/index.jsp Listing of all public implementations: http://www.chemaxon.hu/forum/forum28.html Marc Baaden baaden],[smplinux.de wrote: >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 > > > -- Alex Allardyce Communications Director Chemaxon Ltd Máramaros köz 3/a Budapest, 1037 Hungary Tel.: +361 4532658 Fax.: +361 4532659 e-mail: aa,+,chemaxon.com --------------080901090202000804040304 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI Marc,

ChemAxon have a range of products for core cheminformatics and drug discovery. We made all products free for academic teaching and research. You can find out more here about the conditions here (http://www.chemaxon.hu/forum/ftopic193.html). I list below the main tool classes

Hope it's useful

Cheers / Alex

ChemAxon toolkits currently available
Implementations on our website (Java required):
Marvin and Calculator Plugin (unlimited structure based predictions for pKa, logP, logD, polar surface area (PSA), charge distribution, polarizability prediction, H-bond aceptor/donor, tautomer, resonance, major microspecies, reactivity, refractivity and elemental analysis) :http://www.chemaxon.com/demosite/marvin/index.html
MarvinSpace: http://www.chemaxon.com/shared/MarvinSpace/index.html
JChem: http://www.jchem.com/index.html?content=examples.html
Reactor: http://www.jchem.com/examples/reactor/jsp/index.jsp
Listing of all public implementations: http://www.chemaxon.hu/forum/forum28.html


Marc Baaden baaden],[smplinux.de wrote: 
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

  

-- 
Alex Allardyce
Communications Director

Chemaxon Ltd
Máramaros köz 3/a
Budapest, 1037 Hungary
Tel.: +361 4532658
Fax.: +361 4532659

e-mail: aa,+,chemaxon.com
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