From owner-chemistry@ccl.net Wed Nov 17 08:36:00 2010 From: "Alex Allardyce aa+*+chemaxon.com" To: CCL Subject: CCL: chemicalize.org free service: search added, moves to beta Message-Id: <-43175-101117065439-12693-2Hv3/C18EXt/SK4uSNeBIQ()server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------090907090403010100020206" Date: Wed, 17 Nov 2010 12:54:31 +0100 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa ~ chemaxon.com] This is a multi-part message in MIME format. --------------090907090403010100020206 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Excuse cross postings: Just to let you all know that we have added chemical search to the chemicalize.org site. The search let's you draw, upload a structure or name a molecule as input and perform various structure searches (substructure, exact match and similarity) against the structures identified from web pages already 'chemicalized' by users and see the resulting structures (with the query highlighted in the result). From each result structure you can go on to see a list of web pages where the target structure was included. An elegance is that you can also see other structures on the listed pages and select popular or diverse selection, to understand if the page is chemically relevant before you visit the link. Feedback from test users was very positive especially because they can chemically search 'a significant proportion' of Wikipedia. Other features added include: Auto-complete, structure images for all auto-complete names and roll over large versions of structure images. The name to structure parser is also improved to increase conversion rate and remove error. For more information see this demo video at the site (http://www.youtube.com/watch?v=sF8s44Ha79Y) or this presentation (https://www.chemaxon.com/library/ugm-presentations/2010-usugm/naming-and-chemicalize-org/) of chemicalize.org and the underlying technologies used from our recent US UGM. Hope this is useful -- *Alex Allardyce* Marketing Dir. *ChemAxon**Ltd*. Maramaros koz 3/A, Budapest, 1037 Hungary http://www.chemaxon.com Tel: +361 453 0435 Fax: +361 4532659 mailto:aa:-:chemaxon.com --------------090907090403010100020206 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Excuse cross postings:

Just to let you all know that we have added chemical search to the chemicalize.org site.

The search let's you draw, upload a structure or name a molecule as input and perform various structure searches (substructure, exact match and similarity) against the structures identified from web pages already 'chemicalized' by users and see the resulting structures (with the query highlighted in the result).

From each result structure you can go on to see a list of web pages where the target structure was included. An elegance is that you can also see other structures on the listed pages and select popular or diverse selection, to understand if the page is chemically relevant before you visit the link. Feedback from test users was very positive especially because they can chemically search 'a significant proportion' of Wikipedia.

Other features added include: Auto-complete, structure images for all auto-complete names and roll over large versions of structure images. The name to structure parser is also improved to increase conversion rate and remove error.

For more information see this demo video at the site (http://www.youtube.com/watch?v=sF8s44Ha79Y) or this presentation (https://www.chemaxon.com/library/ugm-presentations/2010-usugm/naming-and-chemicalize-org/) of chemicalize.org and the underlying technologies used from our recent US UGM.

Hope this is useful
--
Alex Allardyce
Marketing Dir.
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +361 453 0435
Fax: +361 4532659
mailto:aa:-:chemaxon.com
--------------090907090403010100020206-- From owner-chemistry@ccl.net Wed Nov 17 11:44:00 2010 From: "Anna Kuzak a.kuzak\a/fqs.pl" To: CCL Subject: CCL: New Cell Illustrator 5.0 release Message-Id: <-43176-101117110919-19068-V2krR9zCct+W7wrobbVq0A_-_server.ccl.net> X-Original-From: Anna Kuzak Content-Type: multipart/alternative; boundary="------------080300020903070400050804" Date: Wed, 17 Nov 2010 17:09:09 +0100 MIME-Version: 1.0 Sent to CCL by: Anna Kuzak [a.kuzak!A!fqs.pl] This is a multi-part message in MIME format. --------------080300020903070400050804 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear All, I am happy to inform you about the new release of Cell Illustrator On-line, version 5.0. I hope you will find it useful in your work. Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. Moreover Cell Illustrator allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins. Cell Illustrator models are used to visualize biological pathways, interpret experimental data and test hypotheses. In addition, it provides researchers with model diagrams of publication quality and simulation result charts. To try the new version please register at: https://cio.bioillustrator.com/cionlineserver/apps/usersman/main New features include: New User Interface; Simulation Engine Enhancements; Unified Gene Net and Bio-pathway; Updates in Element Lists, Graph Layout, CSMLDB Search; CSMLPipeline; Curated Executable Macrophage Database; Data Assimilation. For the details please visit: http://www.cellillustrator.com/new_version/ I hope you will find the software a helpful tool in your work. Regards, Anna Kuzak Key Account Manager Computational Chemistry Software Team FQS Poland Sp. z o.o. (Fujitsu Group), Tel.: (+48 12) 429 43 45 , Fax: (+48 12) 429 61 24, e-mail: ccs##fqs.pl, URL: http://www.fqs.pl/ --------------080300020903070400050804 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear All,

I am happy to inform you about the new release of Cell Illustrator On-line, version 5.0. I hope you will find it useful in your work.

Cell Illustrator is a software tool that enables biologists to draw, model, elucidate and simulate complex biological processes and systems. Moreover Cell Illustrator allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways as well as dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins. Cell Illustrator models are used to visualize biological pathways, interpret experimental data and test hypotheses. In addition, it provides researchers with model diagrams of publication quality and simulation result charts.

To try the new version please register at:
https://cio.bioillustrator.com/cionlineserver/apps/usersman/main

New features include: New User Interface; Simulation Engine Enhancements; Unified Gene Net and Bio-pathway; Updates in Element Lists, Graph Layout, CSMLDB Search; CSMLPipeline; Curated Executable Macrophage Database; Data Assimilation.

For the details please visit:
http://www.cellillustrator.com/new_version/

I hope you will find the software a helpful tool in your work.

Regards,
Anna Kuzak
Key Account Manager
Computational Chemistry Software Team

FQS Poland Sp. z o.o. (Fujitsu Group),
Tel.: (+48 12) 429 43 45 , Fax: (+48 12) 429 61 24, e-mail: ccs##fqs.pl, URL: http://www.fqs.pl/


--------------080300020903070400050804-- From owner-chemistry@ccl.net Wed Nov 17 14:41:01 2010 From: "Sergio Emanuel Galembeck segalemb-.-usp.br" To: CCL Subject: CCL: How to analyze a series of conformers Message-Id: <-43177-101117144017-24773-MSquwZAphOneGZ3KEO+lqA~!~server.ccl.net> X-Original-From: Sergio Emanuel Galembeck Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Wed, 17 Nov 2010 17:40:09 -0200 MIME-Version: 1.0 Sent to CCL by: Sergio Emanuel Galembeck [segalemb]_[usp.br] Hello, I am doing a conformational analysis of an organic molecule. After the conformer generation and geometry optimization I obtained 38 low energy conformers. What is the best idea to analyze them, grouping conformers with similar conformations? Are there some free software that make this kind of analysis? Some years ago I did a work that used clustering techniques, but now I am curious if there are other techniques to do this kind of analysis. Thanks, Sergio Emanuel Galembeck