- chemweb - imperial.ac.uk

Substructure searchable chemistry journals
by Wendy Warr 13 May '05

13 May '05

Is the Journal of Heterocyclic Chemistry really the first substructurally searchable chemistry journal (see below)? Incidentally, I notice a letter in this week's issue of C&EN pointing out that Organic Syntheses, not Beilstein JOC, is the first major Open Access journal in its field. 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 -----Original Message----- From: Organic Chemistry Newsletter [mailto:newsletter@organicworldwide.net] Sent: 29 April 2005 17:48 To: wendy(a)warr.com Subject: Issue 4.04 <http://www.organicworldwide.net/pic/banner_newsletter.jpg> Welcome to Issue 4.04 of the "Organic Chemistry e-Newsletter". A newsletter for industrial/academic organic and medicinal chemists. _____ In this issue: 1. Carbohydrate Synthesis <> 2. Molecules of the Month <> (April 2005) 3. Upcoming Organic Synthesis Conferences <> (May 2005) 4. First Substructure Searchable Chemistry Journal <> 5. Book of the Month <> Distribution: 1418 If you are interested to increase the profile of your product or company by advertising, it is possible to reserve sponsorship for future newsletters. Please contact us <mailto:advertising@organicworldwide.net> to learn more. 1. Carbohydrate Synthesis As carbohydrates have numerous functions in living organisms, the synthesis of oligosaccharides or glycocunjugates for screening is receiving a growing interest. The access to this value-added directory is free during the month May for the readers of this newsletter. user name: guest password: freetrial Carbohydrate <http://www.organicworldwide.net/> Synthesis (under heading Compound Classes) 2. Molecules of the Month (April 2005) Niacin (Vitamin B-3): helps the digestive system, skin, and nerves to work properly and assists in converting food to energy. Sudan 1: red dye used in waxes and polishes, banned for food use. Carbon Monoxide: odorless, colorless gas that interferes with the delivery of oxygen in the blood to the rest of the body. It is produced by the incomplete combustion of fuels. http://www.chemistry.org Serotonin: A molecule of happiness. http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm <http://www.bris.ac.uk/Depts/Chemistry/MOTM/motm.htm> Muraglitazar: a PPAR agonist. PPAR (peroxisome proliferator-activated receptor) is an important target for the treatment of type 2 diabetes, obesity, cardiovascular disease, metabolic syndrome and other human health disorders associated with high intake of dietary fat. http://www.prous.com/mom/mom.asp 3. Upcoming Organic Synthesis Conferences (May 2005) 15th Noordwijkerhout-Camerino Symposium, Trends in Drug <http://www.chem.vu.nl/far/NWC2005/frame.html> Research May 8-13, Noordwijkerhout, The Netherlands 4. First Substructure Searchable Chemistry Journal The Journal of Heterocyclic Chemistry is the first chemical journal to be fully (sub)structure searchable (articles from 1964 to 2001, over 100,000 structures). Journal of <http://www.jhetchem.com> Heterocyclic Chemistry 5. Book of the Month Synthesis of Naturally Occurring Nitrogen Heterocycles from Carbohydrates El Sayed El Ashry, Ahmed El Nemr, ISBN: 1405129344 (Hardcover), 464 pages, Blackwell Publishing, April-May 2005 Publisher <http://www.blackwellpublishing.com/book.asp?ref=1405129344&site=1> Information _____ FEEDBACK We welcome your feedback and questions regarding the Organic Chemistry e-newsletter. In order to ensure a timely response to your inquiry, please e-mail your feedback and questions to newsletter(a)organicworldwide.net. TELL A COLLEAGUE Please take a moment to introduce http://www.organicworldwide.net to your colleagues by forwarding this e-mail. SUBSCRIBE YOURSELF If this message was forwarded to you and you'd like to receive the FREE monthly newsletter directly, you can subscribe here <http://www.organicworldwide.net/newsletter.php> . ARCHIVE To read the past issues of this newsletter, follow this link <http://www.organicworldwide.net/archive.html> and use following access details: user name: organic and password: newsletter UNSUBSCRIBE You have received this message because you indicated that you'd like to receive the newsletter. If you would like to cancel your newsletter subscription, please send us an e-mail at newsletter(a)organicworldwide.net indicating your unsubscription request. _____ Copyright (c) 2005 EcoSynth, Koen Van Aken Ed.

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Focus issue of JCIM - escience
by Wendy Warr 22 Apr '05

22 Apr '05

Dear Colleague, Later this year I will be editing a special issue of the Journal of Chemical Information and Modeling (formerly J. Chem. Inf. Comput. Sci.) with a focus on collaboratories, virtual laboratories, grid computing and other e-science issues. I aim to contact all the best teams in this field with a view to getting them to submit a manuscript, with a deadline of September 1, 2005. I am hoping for a publication date early in 2006; papers would appear on the Web from the end of 2005. The Web manuscript submission page is at https://paragon.acs.org/paragon/index.jsp. It is important that you state in your cover letter that your paper is for my focus issue on e-science. Manuscripts will be peer reviewed, of course, so I cannot promise publication: only contributions that meet the usual standards of JCIM will be accepted. I am writing to you to encourage you to submit a manuscript and to help me publicize this exciting venture. I do hope that you will be interested in giving me your support. Sincerely yours, Dr. Wendy A. Warr Associate Editor, ACS Journal of Chemical Information and Modeling 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

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(Q)SAR in Today's Agrochemistry
by Wendy Warr 30 Mar '05

30 Mar '05

Bob Clark has asked me to draw your attention to this upcoming symposium: A symposium is being organized for this fall's ACS meeting in Washington DC (Aug 28-Sep 1, 2005) entitled: (Q)SAR in Today's Agrochemistry The discovery and development of any biologically active small molecule necessarily entails biological or biochemical testing of candidate compounds and relating the results obtained from such testing back to chemical structure, i.e., establishing structure activity relationships (SARs). This symposium will embrace application of qualitative as well as quantitative analytical methods to agrochemical problems in particular and to in vivo (or ex vivo) assays in general, as well as lead identification (triage) techniques. Talks related to the design of primary and secondary screens will also be appropriate, particularly as they relate to the ability to subsequently carry out meaningful SAR analysis. Many of the difficulties encountered in constructing structure-activity relationships using agrochemical data are also encountered by those in pharmaceutical discovery and development who work, as is more and more common, with whole cell assays. This includes many of the environmental, toxicological and ADME screens now in use in both industries. The symposium is being organized to provide a forum for those with experience in this general realm to share what they have learned with those coming from a more enzyme-based SAR background. Papers involving agrochemical applications are especially encouraged, but any discussion of the challenges that arise in similar applications - e.g., whole cell and intact animal assay systems - are invited as well. Please submit abstracts directly to the OASYS system: http://oasys.acs.org/acs/230nm/agro/papers/index.cgi The deadline for abstract submission is April 26, 2005. Bob Clark Tripos, Inc. 1699 S. Hanley Rd. St. Louis MO 63144 bclark(a)tripos.com 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

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xqDoc
by Wendy Warr 29 Mar '05

29 Mar '05

This was in the Managing Information newsletter: "Elsevier has revealed a new open source cross-referencing tool for XQuery applications, called xqDoc, developed by Darin McBeath, an Elsevier employee in the company's Advanced Technology Group. The tool is now freely available to the open source community. XQuery is a new query/programming language based on XML and used in conjunction with XML databases such as MarkLogic, a commercial database, and eXist, on the open source side. The goal of xqDoc is to provide a vendor neutral solution for documenting XQuery applications, as well as tools to generate a user-friendly representation of this documentation and cross-referencing information (e.g., how different functions are used by each other). This is accomplished through several components, including a new commenting convention that extends the currently defined XQuery comment style. This convention is modeled after Java's Javadoc commenting style, and provides a simple, uniform way to document XQuery source code. Javadoc is a widely used tool for providing the same sort of information for Java programs that xqDoc provides for XQuery programs. It is hoped that xqDoc achieves the same level of adoption and success for XQuery that Javadoc has for Java. For further information on xqDoc, visit www.xqdoc.org <http://www.xqdoc.org/> " 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

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On Demand Staffing for Information Technology Projects
by Lionel Zhou 23 Mar '05

23 Mar '05

Rent-A-Pro.com offers on demand staffing and service delivery for information technology projects. It is convenient for small businesses as well as individual developers to get temporary help, consulting service and outsourcing service from independent contractors around the world through our site. We provide functions for posting project requirements, bidding for projects, rating between buyers and sellers. Buyers and sellers are protected from fraud by an escrow system and a dispute resolution system. http://www.rent-a-pro.com/

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Molecular Workbench
by Rzepa, Henry 04 Mar '05

04 Mar '05

I recommend a visit to <http://workbench.concord.org/modeler/index.html>http://workbench.concord.org/modeler/index.html Or, Launch MW by clicking on the following link:<http://xeon.concord.org:8080/modeler/webstart/MW.jnlp>http://xeon.concord.org:8080/modeler/webstart/MW.jnlp -- Henry Rzepa. +44 (020) 7594 5774 (Voice); +44 (0870) 132 3747 (eFax); rzepahs(a)mac.com (iChat) http://www.ch.ic.ac.uk/rzepa/ Dept. Chemistry, Imperial College London, SW7 2AZ, UK. (Voracious anti-spam filter in operation for received email. If expected reply not received, please phone/fax).

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Molecule of the Month - March
by Paul May 01 Mar '05

01 Mar '05

Hi, March's MOTM is hexenal, the smell of newly mown grass. It has been written by Simon Cotton from Uppingham School, Rutland, UK, and various enhanced versions of the page are available. http://www.chm.bris.ac.uk/motm/motm.htm#mar2005 regards, ---------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, BRISTOL BS8 1TS, UK tel: +44 (0)117 9289927 fax: +44 (0)117 9251295 mobile: +44(0)7811371539 Email: Paul.May(a)bristol.ac.uk Web: http://www.chm.bris.ac.uk/staff/pwm.htm MOTM: http://www.chm.bris.ac.uk/motm/motm.htm "Dopeler effect: The tendency of stupid ideas to seem smarter when they come at you rapidly" ----------------------------------------------------------------------------

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Chemical Information and Computation
by Wendy Warr 20 Feb '05

20 Feb '05

CHEMICAL INFORMATION AND COMPUTATION 2004, NUMBER 2 Report on the 228th ACS National Meeting and Exposition Our report on the Fall National Meeting of the American Chemical Society, held in Philadelphia, will be available before the end of February. It . includes news from about 70 companies (including some not exhibiting) . covers press releases for the last six months of 2004 . features write-ups of 37 papers (all of them author-checked) covering . cheminformatics in 2D (the Herman Skolnik Award symposium honoring Peter Johnson) . advances in virtual high throughput screening . scholarly publishing: initiatives and electronic publishing . scholarly publishing: challenges for peer review in the digital world . scholarly publishing: perspectives on Open Access . open meeting of the ACS committees on ACS Publications and CAS (Contents list in full at http://www.warr.com/morepubs.html.) 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

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Need help for publication of simple softwares about CADD
by Sheng-Hung Wang 15 Feb '05

15 Feb '05

Dear all, I am a Ph.D student at Graduate Institute of Pharmaceutical Chemistry in Taiwan. I developed some simple tools about CADD, as you can see them here: http://home.pchome.com.tw/team/gentamicin/mol/mol.htm I did not publish these softwares in any journal. But people who apply these tools in their researches, sometimes hope or need to know how to cite a reference in their publications. Actually, my major study field is pharmaceutical chemistry, not computational chemistry or bioinformatics. And these programs are just "simple tools". So, I think I need to find coworkers who are in these fields to publish the programs. Or somebody who interests these programs, you can include these programs to your research and public them together. Any suggestions or any kinds of help are greatly appreciated. Yours sincerely, Sheng-Hung Wang Candidate for Doctor's Degree Graduate Institute of Pharmaceutical Chemistry China Medical University 91 Hsueh-Shih Rd. Taichung, Taiwan, ROC gentamicin5(a)yahoo.com.tw _______________________________________________________________________ Yahoo!奇摩電子信箱免費容量250MB，信件在多也不怕 http://tw.promo.yahoo.com/mail_new/index.html

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Molecule of the Month - February
by Paul May 01 Feb '05

01 Feb '05

Hi, February's MOTM is Galactosylceramide, which is a chemical found in the brain which is a constituent of nerve cells and intestinal membranes - and which may be implicated in promoting diseases such as HIV. It has been written by prof Jacques Fantini of the Université Paul Cézanne Marseille, France. http://www.chm.bris.ac.uk/motm/motm.htm#feb2005 (I only have a few MOTMs waiting at the moment, and they are all by the same couple of authors, so if any of you would like to contribute a MOTM about an interesting molecule, please let me know). regards, ---------------------------------------------------------------------------- Dr Paul May, School of Chemistry, University of Bristol, BRISTOL BS8 1TS, UK tel: +44 (0)117 9289927 fax: +44 (0)117 9251295 mobile: +44(0)7811371539 Email: Paul.May(a)bristol.ac.uk Web: http://www.chm.bris.ac.uk/staff/pwm.htm MOTM: http://www.chm.bris.ac.uk/motm/motm.htm "If brute force doesn't work, you're not using enough of it" ----------------------------------------------------------------------------

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