- chemweb - imperial.ac.uk

What is Cheminformatics?
by Dr. Wendy A. Warr 27 Nov '99

27 Nov '99

Please excuse duplicate postings. My thanks to everyone who sent me data, opinions, and job descriptions for my talk in New Orleans on the discipline of cheminformatics and the shortage of skilled staff in that field. I promised to summarize it all for the lists but that is very difficult in view of the sheer volume of information involved. About two years ago, many people (including myself) considered that "cheminformatics" was a nasty neologism. My survey this summer shows that it is now an established discipline, although the tasks involved, and even the name of the discipline, are not clearly defined yet. "Cheminformatics" was preferred to "chemoinformatics" by most respondents. One company uses "chemiiinformatics". There is still much distaste for the job title "cheminformatician". A zipped file of my PowerPoint slides is available on my Web site http://www.warr.com/ I have been waiting for COMP Division to put all the slides from this Symposium on the COMP web site at http://membership.acs.org/C/COMP/ Unfortunately I think that this has not happened - though at least four of the main headings on that home page give "404 Not Founds", so perhaps the material is there but temporarily hidden. My sincere thanks to all of you who helped in this survey. Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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PowBase : Powder Patterns Database
by Armel Le Bail 09 Nov '99

09 Nov '99

A new free-access database of constant-wavelength powder diffraction patterns, PowBase, is searchable online at : http://sdpd.univ-lemans.fr/powbase/ The current content is already 81 patterns (conventional X-ray, synchrotron, neutron) presenting typical cases for high or low resolution, line broadening effects, standard materials, ab initio structure determination, etc. This is almost 3% of the future ICDD PDF-3 commercial database after 6 days of existence. Enlarging the base depends on you. Send your data, published or not, inorganic as well as organic ! Armel Le Bail http://www.cristal.org/ chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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Re: WebMolecules
by Phil Stevens 09 Nov '99

09 Nov '99

"Dr. Wendy A. Warr" wrote: > > We had a message from Wolf-Dietrich Ihlenfeldt in August about products > from Molecular Arts Corporation that fail to acknowledge his group. Can > anyone tell us if this latest offering is ethically acceptable? As a matter of company policy, we make a good faith effort to contact all parties whose prior work contributed in any significant way to our commercial products. If the work is considered even remotely sublicensable and the author is willing, we arrange for same at our expense before letting our developers dig in. If the prior work is recently in the public domain or from recently published data, we still seek to secure permission for any attribution for same from those who are interested in doing so. In our view, the ethical problems of using prior works to lend unsubstantiated credence to new commercial development is of some significance. If there is no response, we assume that there is no interest in having us make an attribution and therefore we remain silent on that issue. In particular we do not make any quality assertions regarding that issue so as to avoid taking inadvertent credit for specific results. Believe me, I would much rather have products with a long list of referenced articles after them (and many of our products do). However, without such, our products can only stand or fall on their own. Lastly, we have not received any complaint from Dr. Ihlenfeldt either in public or private. Any complaint about our products receives my immediate attention. Did something slip by me? Apparently. We also have a designated company ethicist and we routinely cover these types of issues to make sure someone here doesn't get too far ahead of themselves. Now this is not to say we have covered all our bases, but we do honestly try. It makes no sense for us to upset any potential customer. If you are aware of a problem, please contact me offline or have the affected party get in touch with us so that we may resolve it quickly. Given the above, I would say our ethics are at least as good as those of someone who would question our ethics in public without having contacted us first. Sincerely, -- Phil Stevens Molecular Arts Chemistry and Safety Software for the Classroom, Lab, and Field ---------------------------------------------------------------- Molecular Arts Corporation | <phils(a)molecules.com> Hanover Corporate Centre, Suite 1000 | http://www.molecules.com 1532 East Katella Avenue | Main: (714) 634-8100 Anaheim, California 92805-6627 USA | FAX: (714) 634-1999 ---------------------------------------------------------------- -- Phil Stevens Molecular Arts Chemistry and Safety Software for the Classroom, Lab, and Field ---------------------------------------------------------------- Molecular Arts Corporation | <phils(a)molecules.com> Hanover Corporate Centre, Suite 1000 | http://www.molecules.com 1532 East Katella Avenue | Main: (714) 634-8100 Anaheim, California 92805-6627 USA | FAX: (714) 634-1999 ---------------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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WebMolecules News - Nov 99
by Phil Stevens 08 Nov '99

08 Nov '99

A new version of the award-winning site: ** WebMolecules.com ** is now available at http://www.webmolecules.com Visualize molecules in 3D - real-time on the Web! New Features: -------------------------------------------------------------- - Another 50,000 CAS-indexed molecular models have been added. We now have over 100,000 molecular models on-site. Search for these by CAS number http://www.webmolecules.com/search.shtml - New Visitor Uploads are available in Category 28.0 Includes the Fun, the Unusual, and the Unclassifiable. - Email Models to Friends You can now send 3D models to friends via email. When viewing a 3D model, just click the Email Model link. Molecule du Jour -------------------------------------------------------------- Hexamethylphosphoramide (HMPA) http://www.webmolecules.com/cgi-bin/webmolpage.cgi?hmpa.m3d Formula: C6H18N3OP Weight: 179.202(1) g/mol Colorless liquid Patented by Monsanto - 1956 Solvent for polymers; polymer UV protectant additive; jet fuel de-icing additive; chemosterilant (insects); probable carcinogen; known mutagen Other Recent Upgrades and New Features -------------------------------------------------------------- - 100's of large structures have been added. For example: DNA, RNA, C180, C240, cyclodextrin, vitamin B12, large nanotech models, crystals, etc. - Support for both Chime and VRML plug-ins - For performance reasons, large molecules (>150 atoms) are available for the Chime viewer only. - Mirror sites for the VRML plug-ins have been added. See: http://www.webmolecules.com/vrmlint.shtml - Mirror sites for the Chime plug-in has been added. See: http://www.webmolecules.com/chimeint.shtml - Resizable viewing window - Support for uploads and model requests - Improved support for bookmarks - 3D coordinate downloads (M3D, MOL, PDB) -------------------------------------------------------------- WebMolecules.com is a FREE, sponsor-supported site. Designed for the 3D visualization of molecules, it contains over 100,000 molecular structures in 3D. Thousands of common molecules are organized into 30+ categories. Included are molecules of commercial value, educational importance, and of topical interest. It is indexed by formula and category and is also fully searchable. Included are structures such as: - Top 100 pollutants - Top 100 commercial chemicals - Top 200 pharmaceuticals - Common valence geometries - Common orbital configurations WebMolecules.com is great for student and classroom use. -------------------------------------------------------------- KNOW SOMEONE WHO MIGHT ENJOY WEBMOLECULES? Feel free to forward WebMolecules News to your colleagues. If you received this issue from a friend and would like to receive information directly, you can join our mailing list by clicking the Free Newsletter link at: http://www.webmolecules.com or better yet, tell them to sign-up directly on: http://www.webmolecules.com/newsletter.shtml -------------------------------------------------------------- Enjoy. -- Phil Stevens <phils(a)webmolecules.com> http://www.webmolecules.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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MolMall - Rare Chemical Samples Database on the Internet
by Shu-Kun Lin 05 Nov '99

05 Nov '99

You may easily search for samples you need at MolMall (http://www.molmall.org) the Rare Chemical Samples Exchange Center. You may do full structure search or substructure search on the website. You may search for name of the submitter. E.g., at "Power Search", you put LIN as the query, you will find a list of 8 structures (Lin contributed 8 samples). There other very useful searching functions. More detailed data sheet regarding a sample is available by clicking on the number. Direct link to published paper was made. However, so far there are only links to Molecules MolBank (http://www.molbank.org) papers if the compounds are published there. We also plan to allow he sample submitters to add additional information to the data sheet, such as the literature where the compound was published. Any suggestions? Have fun! Shu-Kun -- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland Tel. +41 79 322 3379, Fax +41 61 302 8918 E-mail: lin(a)mdpi.org http://www.mdpi.org/lin/ chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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News items
by Dr. Wendy A. Warr 04 Nov '99

04 Nov '99

Some recent news items at http://www.warr.com/warrzone.htm Argonaut and Symyx Sell Instruments for Combinatorial Chemistry Spotfire and Oxford Molecular Group Integrate Software Oxford Molecular launches RS3 Discovery for Excel Cambridge Combinatorial Announces Name Change Alliance of Cambridge Discovery Chemistry and Lancaster Synthesis News from LHASA Ltd Intranet International 2000: a New Conference Announced Annual General Meeting of the Pharma Documentation Ring Roche, Parke-Davis and Ribotargets Award Additional Contracts To Biofocus Annual Reports in Combinatorial Chemistry and Molecular Diversity ChemConnect Announces Successful Second Round of Capital Funding Beilstein Abstracts Now Free of Charge to Members of ChemWeb.com ChemWeb Launches Catalysis Forum New Version of Marvin Java Applets Latest Issue in the Current Trends Series Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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November Molecule of the Month - Tetrodotoxin
by Paul May 31 Oct '99

31 Oct '99

Hi, November's MOTM is Tetrodotoxin, the potent nerve agent found in puffer fish. It has been written by Jim Johnson from a company called 3D Biochem in the US who make molecular models for schools & universities. All 4 formats are available (HTML, Chime, Java-Chemsymphony and VRML): http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm Regards, ------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, UK tel: +44 (0)117 928-9927, fax: +44 (0)117 925-1295 <mailto:paul.may@bris.ac.uk> <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> "If a packet hits a pocket on a socket on a port, and the bus is interrupted as a very last resort, and the address of the memory makes your floppy disk abort, then the socket packet pocket has an error to report." Dr Suess. ------------------------------------------------------------------------- chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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chemsoc choice award
by Dr. Wendy A. Warr 29 Oct '99

29 Oct '99

We are pleased to announce our first chemsoc Choice Award to Professor Joseph Hornak's site The Basics of NMR, accessible at http://www.cis.rit.edu/htbooks/nmr/nmr-main.htm This site was recommended by Robert Michaelson. For more details, including a site review, visit http://www.chemsoc.org/gateway/chembyte/choiceaward.htm Wendy -- Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 wendy(a)warr.com http://www.warr.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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Re: One-Wedge Convention for Stereochemical Representation, Proposal
by Jonathan Brecher 22 Oct '99

22 Oct '99

At 1:39 PM -0400 10/22/99, Richard B. Silverman wrote: >I don't want to put a damper on your nomenclature, but I am quite happy >with the nomenclature as it stands. I have no problem if some people use a >decreasing hatched wedge or increasing hatched wedge to symbolize away from >the plane. To understand the one-wedge nomenclature it requires a special >set of new rules to learn (the students will hate you). Because solid and >hatched wedges are used in other disciplines to represent closer than and >farther than, respectively, everyone already knows this nomenclature. I >think that this is an unnecessary addition to organic chemistry. I'm afraid I agree with Dr. Silverman. What problem are you trying to solve? Y cn ndrstnd sntncs wrttn wtht vwls, bt wh wld y wnt t? Jonathan Brecher CambridgeSoft Corporation jsb2(a)camsoft.com chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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One-Wedge Convention for Stereochemical Representation, Proposal
by Shu-Kun Lin 22 Oct '99

22 Oct '99

Dear colleagues: We have prepared a proposal on "One-Wedge Convention for Stereochemical Representation" at http://www.mdpi.org/molecules/wedge/ This convention, if followed by all the chemists, will be very useful. Without a convention of graphic representation, the situation of stereochemistry representation is now very much similar to the nomenclature situation before the CIP rule of stereochemical nomenclature was proposed. Could you please take a look at the first draft of this proposal at the http://www.mdpi.org/molecules/wedge/ website? We would greatly appreciate it if you offer some suggestions. Any of your chemsists who improve it further will be invited to be coauthors. Best regards, Shu-Kun Lin, lin(a)mdpi.org Luc Patiny, Luc.Patiny(a)ico.unil.ch -- Dr. Shu-Kun Lin Molecular Diversity Preservation International (MDPI) Saengergasse 25, CH-4054 Basel, Switzerland Tel. +41 79 322 3379, Fax +41 61 302 8918 E-mail: lin(a)mdpi.org http://www.mdpi.org/lin/ chemweb: A list for Chemical Applications of the Internet. To post to list: mailto:chemweb@ic.ac.uk Archived as: http://www.lists.ic.ac.uk/hypermail/chemweb/ To (un)subscribe, mailto:majordomo@ic.ac.uk the following message; (un)subscribe chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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