- chemweb - imperial.ac.uk

Molecule of the Month - February
by Paul May 01 Feb '04

01 Feb '04

Hi, February's MOTM is Combretastatin, which is a Zulu poison that is now being used as a possible cure for cancers. It has been written by Mike Thompson of Uppingham School. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#feb2004 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> Mobile: 07811371539 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------

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Chemistry Wiki
by Mark Winter 15 Jan '04

15 Jan '04

Henry's recent note reminds me of his earlier note about the wiki concept and so I'd like to point out that WebElements now has a (largely unpopulated) "wiki" at http://www.webelements.com/wiki/ ChemWiki: Chemistry web pages in continual change as a result of efforts by the users. Eventually (hopefully) you will find pages about many aspects of chemistry here - and if you like you can edit them, and add new pages as well. That's the idea in fact. While WebElements is a periodic table thing, I've put a framework in to try and encourage the build up of any chemistry themes. Editing is easy and uses a highly simplified system for adding headings, bold/italics, etc. I do ask that anyone interested might like to try it out by adding a few snippets of information perhaps. It will be interesting to see how chemists react to a wiki. Slowly with a high activation energy I suspect. The site has been live for nearly a month and the stats show many have browsed around it - but that users seem shy about actually adding information. Henry also encouraged chemists to consider providing news feeds a while ago. In that spirit news junkies can see which chemwiki pages are updated via the feed at http://www.webelements.com/wiki/index.php?action=rss Other feeds for the WebElements "blog" and the WebElements forum are at http://www.webelements.com/news/xml-rss.php and http://www.webelements.com/forums/rss.php Please do offer feedback! Regards -- Dr Mark J Winter Department of Chemistry, The University, Sheffield S3 7HF, England tel: +44 (0)114 222 9304 fax: +44 (0)114 222 9303 e-m: mark.winter(a)sheffield.ac.uk http://www.shef.ac.uk/chemistry/staff/mjw/mark-winter.html WebElements is the periodic table on the world-wide web: http://www.webelements.com/ The Sheffield Chemdex is a listing of chemistry sites on the world-wide web: http://www.chemdex.org/

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The Chemical Internet at "10" ?
by Rzepa, Henry 15 Jan '04

15 Jan '04

The "10th" birthday of the "web" passed mostly without comment in 1999; I mention this since arguably 2004 (perhaps Jan, perhaps May) would represent such for "chemistry". So it might be useful to ask people on this list for any comments, eg along the lines of what have been the significant changes in the way we "do" chemistry as a result of the last ten years! Given that many of us have opinions of where we would like to be, in an ideal world, with the chemical Internet, it is all to easy to look at some trends, and say "not there yet". One "not yet there" aspect which I encountered yesterday was what I call "TQA-induced" activity (TQA is the UK-speak quality assessment exercise that some chemistry depts hare undergoing in 2004). A policy came down from upon high that we should ensure that our students would have online access to as many teaching materials as we could manage for the TQA. Accordingly, a steady stream of such has been arriving on my desk (as coordinator of such). Opening up e.g. the latest, I was intrigued to find a collection of Acrobat files, many ranging in sizes between 6-14 Mbytes. This size-induced Web unfriendliness probably originates in many ways, one of which may well be clipboard-pasted graphics, probably at very high resolution, which gets distilled in with no compression by time-pressed secretaries (or even worse, simply produced from flatbed scanners). Indeed Acrobat (sometimes copy protected, rarely accompanied by the "source document") seems increasingly ubiquitous on the Web; virtually all electronic journals now offer it, e-books using it are starting to appear (I posted on this earlier), and increasingly at the very operating system level, "print to PDF" is offered as an option. Acrobat is an asynchronous medium; it is far easier to produce such, than to use (re-use) it (Acrobat parsers do exist however, but how effective they are I do not know). Thus this frenzy to populate the Internet with chemistry wrapped in Acrobat is very much a one-way (non reusable) mechanism for the digital information it represents. So will we come to see the first 10 years of the chemical Web really just as digital paper, or something much more fundamental? Opinions welcome! -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax)

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FW: ADMET-1 Conference - Detailed program information (fwd)
by Wendy Warr 05 Jan '04

05 Jan '04

...with apologies for duplicate postings. Wendy ---------- Forwarded message ---------- Date: Sun, 4 Jan 2004 21:08:30 -0500 (EST) From: Steve Heller <steve(a)hellers.com> To: CHMINF-L(a)indiana.edu Cc: Steve Heller <steve(a)hellers.com> Subject: ADMET-1 Conference - Detailed program information Please plan to attend the ADMET-1 Conference. ADMET-1 will be held February 11-13, 2004 in San Diego, California. For more information, see the Conference URL: http://www.scherago.com/admet ADMET-1 will be an international meeting bringing together leaders in the computational and experimental areas of ADMET. The meeting will consist of invited lectures, poster talks, as well as scientific and vendor workshop presentations. The lectures will focus on theory and application of both computational and experimental ADMET approaches. In addition, lecturers will be asked to mention explicitly how they handle structural diversity and noisy data characteristic of ADMET problems. The deadline for submitting abstracts has been extended to January 20, 2004. --------------------------------------------------------------------- ADMET-1 Conference February 11-13, 2004 Town & Country Hotel San Diego, California http://www.scherago.com/admet Co-Organizers: - Steve Heller, NIST, USA (srheller.gov) - Tony Hopfinger, University of Illinois at Chicago, USA (hopfingr.edu) Organizing Committee: Susan Bassett, Consultant, USA; Kevin Geiss, Wright-Patterson Air Force Base, USA; Osman Guner, Accelyrs, USA; Peter Gund, IBM Life Sciences Pharmaceutical R&D Solutions, USA; Philip Judson, LHASA/University of Leeds, UK; Daniel A Kleier, Dupont, USA; D.J. Livingstone, ChemQuest, UK; Edward Matthews, Food & Drug Administration, USA; Donna Morrall, Proctor & Gamble, USA; Ann M Richard, US Environmental Protection Agency, USA; Patrick Sinko, Rutgers, The State University of New Jersey, USA; Sung-Sau So, Hoffmann-La Roche, USA; Ikumi Tamai, Tokyo University of Science; Gil Veith, US Environmental Protection Agency, USA; David A. Winkler, CSIRO Molecular Science, Australia; Antony Williams, ACD/Labs, Canada; Chihae Yang, Leadscope, USA. Session Topics: - Computational Toxicology - Computational Metabolism/Excretion - Experimental ADMET - Computational Absorption/Distribution Other Sessions, Technical Workshops and Exhibitors: (as of January 2004) - There will also be scientific workshop on Tox-ML. and the Predictive -Scientific Co-Sponsors: COMP - ACS Division of Computers in Chemistry CINF - ACS Division of Chemical Information TOXI - ACS Division of Chemical Toxicology Controlled Release Society (CRS) Corporate Sponsors: Bio-Rad Laboratories Advanced Chemistry Development, Inc. MDL Information Systems, Inc. IBM Exhibitors: Advanced Chemistry Development, Inc. Bio-Rad Laboratories LION Bioscience MDL Information Systems, Inc. Simulations Plus, Inc. Tryverse LHASA Limited Accelrys Leadscope Prous Science Chemical Computing Group, Inc. Speakers (Titles of the talks are available on the web site): Gordon Amidon (University of Michigan), Johnny Gasteiger (University of Erlangen, Germany), Edwin J. Matthews (Food & Drug Administration, USA), Ann Richard (US Environmental Protection Agency, USA), Philip Lee (Dupont, USA), Daniel A. Norris (LION Bioscience, USA), Akira Tsuji (Kanazawa University, Japan), Mike H Abraham (University College London, England), William J. Egan (Vertex Pharmaceuticals, USA), Dhiren Thakker (University of North Carolina, USA) Registration Fees: Students : $200 University/Government: $300 Industry : $400 A registration form can be downloaded from: http://www.intl-pag.org/admet/1/forms/admet1.doc --------------------------------------------------------------------- SCHERAGO INTERNATIONAL - 11 Penn Plaza, Ste 1003, New York, NY 10001 Tel: 1-212-643-1750 ext. 20 / Fax: 1-212-643-1758 Email: admet.com / Website: www.scherago.com/admet ---------------------------------------------------------------------

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RE: [chemweb] Ebooks in chemistry
by Wiggins, Gary D. 17 Dec '03

17 Dec '03

OCLC's netLibrary (http://www.oclc.org/netlibrary/) includes a number of chemistry-related ebooks, some of which are listed below. I believe that in our library system, readers can only read two hours of text at a time. According to the netLibrary web site, eBook checkout times are set by a library's netLibrary administrator and are not set by netLibrary specifically. Gary Wiggins, Indiana University School of Informatics 1. The Riddle of the Rhine : Chemical Strategy in Peace and War by Lefebure, Victor. Charlottesville, Va. University of Virginia Library,, 1996. 2. Religion and Chemistry by Cooke, Josiah Parsons. Charlottesville, Va. University of Virginia Library,, 1997. 3. Biomimetic Sensor Technology by Toko, Kiyoshi. New York Cambridge University Press, 2000. 4. Schaum's Outlines : Theory and Problems of Beginning Chemistry Schaum's Outline Series by Goldberg, David E. New York McGraw-Hill Professional, 1999. 5. Chemistry for Every Kid : 101 Easy Experiments That Really Work Janice VanCleave Science for Every Kid Series by VanCleave, Janice Pratt. New York John Wiley & Sons, Inc. (US), 1989. 6. The Confessions of a Consulting Chemist by Munn, William Faitoute. Boulder, Colo. NetLibrary,, 1996. 7. Schaum's Outline of Theory and Problems of Organic Chemistry Schaum's Outline Series by Meislich, Herbert. New York McGraw-Hill Professional, 1999. 8. Art in Chemistry, Chemistry in Art by Greenberg, Barbara R.; Patterson, Dianne. Englewood, Colo. Teacher Ideas Press, 1998. 9. 1001 Chemicals in Everyday Products by Lewis, Grace Ross. New York John Wiley & Sons, Inc. (US), 1999. 10. Schaum's Easy Outlines. Organic Chemistry : Based On Schaum's Outline of Organic Chemistry By Herbert Meislich, Howard Nechamkin, and Jacob Sharefkin Schaum's Outline Series by Meislich, Herbert.; Nechamkin, Howard; Sharefkin, Jacob New York McGraw-Hill Professional, 2000. 11. Janice Vancleave's A+ Projects in Chemistry : Winning Experiments for Science Fairs and Extra Credit by Vancleave, Janice Pratt. New York John Wiley & Sons, Inc. (US), 1993. 12. Graduate Education in the Chemical Sciences--issues for the 21st Century : Report of a Workshop by Washington, D.C. National Academy Press, 2000. 13. Great Jobs for Chemistry Majors by Rowh, Mark. Lincolnwood, Ill. NTC Contemporary, 1999. 14. Principles of Soil Chemistry Books in Soils, Plants, and the Environment by Tan, Kim H. New York Marcel Dekker, Inc., 1998. 15. Schaum's Outline of Theory and Problems of Beginning Chemistry Schaum's Outline Series by Goldberg, David E. New York McGraw-Hill Professional, 1991. 16. Schaum's Outline of Theory and Problems of College Chemistry Schaum's Outline Series by Rosenberg, Jerome Laib.; Epstein, Lawrence M. New York McGraw-Hill Professional, 1997. 17. Schaum's Outline of Theory and Problems of Organic Chemistry Schaum's Outline Series by Meislich, Herbert.; Nechamkin, Howard; Sharefkin, Jacob New York McGraw-Hill Professional, 1991. 18. Chemistry Today and Tomorrow : The Central, Useful, and Creative Science by Breslow, Ronald. Washington, DC : Boston Jones & Bartlett Publishers, Inc., 1997. 19. Basic Skills for Organic Chemistry : A Toolkit by Rosenfeld, Stuart M. Sudbury, Mass. Jones & Bartlett Publishers, Inc., 1998. 20. Environmental Organic Chemistry : Illustrative Examples, Problems, and Case Studies by Schwarzenbach, René P. New York John Wiley & Sons, Inc. (US), 1995. 21. Water Chemicals Codex by Washington, D.C. National Academies Press, 1982. 22. Medicinal Plants of the World : Chemical Constituents, Traditional, and Modern Medicinal Uses by Ross, Ivan A. Totowa, N.J. Humana Press, 1999. 23. CliffsQuickReview Chemistry Cliffs Quick Review by Nathan, Harold D.; Henrickson, Charles. New York Cliffs Notes, 2001. 24. Organic Chemistry II Cliffs Quick Review by Pellegrini, Frank. Foster City, CA Cliffs Notes, 2000. 25. Quantum Systems in Chemistry and Physics : Granada, Spain, 1998 Progress in Theoretical Chemistry and Physics ; V. 2-3 by Hernandez-Laguna, Alfonso. New York Kluwer Academic Publishers, 2002. 26. How to Solve Word Problems in Chemistry How to Solve Word Problems by Goldberg, David E. New York McGraw-Hill Professional, 2001. 27. Chemical Ecology : The Chemistry of Biotic Interaction by Eisner, Thomas; Meinwald, Jerrold Washington, D.C. National Academies Press, 1995. 28. A History of the International Chemical Industry Chemical Sciences in Society Series by Aftalion, Fred. Philadelphia University of Pennsylvania Press, 1991. 29. From Chemical Philosophy to Theoretical Chemistry : Dynamics of Matter and Dynamics of Disciplines, 1800-1950 by Nye, Mary Jo. Berkeley University of California Press, 1993. 30. Principles of Quantum Mechanics As Applied to Chemistry and Chemical Physics by Fitts, Donald D. New York Cambridge University Press, 1999. 31. The Chemical History of a Candle by Faraday, Michael. Hoboken, N.J. BiblioBytes,, . 32. Chemical Dependency and the Dysfunctional Family Drug Abuse Prevention Library by Biggers, Jeff. New York Rosen Publishing Group, 1998. 33. How to Find Chemical Information : A Guide for Practicing Chemists, Educators, and Students by Maizell, Robert E. New York John Wiley & Sons, Inc. (US), 1998. 34. Cliffs AP Chemistry by Thorpe, Gary S. New York Cliffs Notes, 2001. 35. Assessing the Value of Research in the Chemical Sciences : Report of a Workshop by Washington, D.C. National Academies Press, 1998. 36. Aquatic Chemistry : Chemical Equilibria and Rates in Natural Waters Environmental Science and Technology by Stumm, Werner.; Morgan, James J. New York John Wiley & Sons, Inc. (US), 1996. 37. Every Person's Guide to Antioxidants by Smythies, John R. New Brunswick, N.J. Rutgers University Press, 1998. 38. The Logic of Chemical Synthesis by Corey, E. J.; Cheng, Xue-min. New York John Wiley & Sons, Inc. (US), 1995. 39. Reaction Kinetics Oxford Science Publications by Pilling, M. J.; Seakins, Paul W. Oxford ; New York Oxford University Press (UK), 1995. 40. Chemistry of Non-stoichiometric Compounds Oxford Science Publications by Kosuge, Kåoji. Oxford ; New York Oxford University Press (UK), 1994. 41. A Review of the Scientific Literature As It Pertains to Gulf War Illnesses, Infectious Diseases Gulf War Illnesses Series ; V. 1 by Hilborne, Lee H.; Golomb, Beatrice Alexandra. Santa Monica, Calif. RAND, 2001. 42. Ritalin : Its Use and Abuse Drug Abuse Prevention Library by Beal, Eileen. New York Rosen Publishing Group, 1999. 43. Janice Vancleave's 200 Gooey, Slippery, Slimy, Weird & Fun Experiments by VanCleave, Janice Pratt. New York John Wiley & Sons, Inc. (US), 1993. 44. Patents for Chemicals, Pharmaceuticals, and Biotechnology : Fundamentals of Global Law, Practice, and Strategy by Grubb, Philip W. Oxford : New York Oxford University Press (UK), 1999. 45. Improving Research Capabilities in Chemical and Biomedical Sciences : Proceedings of a Multi-site Electronic Workshop Compass Series (Washington, D.C.) by Washington, D.C. National Academies Press, 1999. Gary Wiggins Director, Program in Chemical Informatics Interim Director, Program in Bioinformatics Adjunct Professor of Informatics School of Informatics 901 East Tenth Street Bloomington, Indiana 47408-3912 Phone: 812-856-1086 Fax: 812-856-4764 E-mail: wiggins(a)indiana.edu -----Original Message----- From: chemweb-bounces(a)imperial.ac.uk [mailto:chemweb-bounces@imperial.ac.uk] On Behalf Of Rzepa, Henry Sent: Wednesday, December 17, 2003 9:27 AM To: chemweb(a)imperial.ac.uk Subject: [chemweb] Ebooks in chemistry The list of chemistry titles at eg http://www.ebooks.com/subjects/88.smm is looking impressive (although at first glance, so are the prices). Has anyone bitten the bullet and recommended etexts for student courses etc (or actually know anyone who has purchased such?) Mind you, when one looks at the formats available for ebooks (http://www.ebooks.com/help/tools/readers.smm) you have to wonder whether it represents a real advance from print. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax) _______________________________________________ chemweb mailing list chemweb(a)imperial.ac.uk http://mailman.ic.ac.uk/mailman/listinfo/chemweb List coordinator, Henry Rzepa (mailto:rzepa@ic.ac.uk)

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Ebooks in chemistry
by Rzepa, Henry 17 Dec '03

17 Dec '03

The list of chemistry titles at eg http://www.ebooks.com/subjects/88.smm is looking impressive (although at first glance, so are the prices). Has anyone bitten the bullet and recommended etexts for student courses etc (or actually know anyone who has purchased such?) Mind you, when one looks at the formats available for ebooks (http://www.ebooks.com/help/tools/readers.smm) you have to wonder whether it represents a real advance from print. -- Henry Rzepa. Imperial College, Chemistry Dept. +44 0778 626 8220 +44 020 7594 5804 (Fax)

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Escher NG 1.0 release
by Giulio Vistoli 17 Dec '03

17 Dec '03

Dear all, We are proud to announce the release of Escher NG 1.0, freely downloadable at www.ddl.unimi.it ESCHER Next Generation (NG) is an enhanced version of the original ESCHER protein-protein automatic docking system developed in 1997 by Gabriele Ausiello, Gianni Cesareni and Manuela Helmer Citterich. The new release, with a reengineered code, includes some new features: - Protein-protein and DNA-protein docking capability. - Fast surface calculation based on the NSC algorithm. No external software are required. - Only two PDB files are required as input. - Parallel code. ESCHER NG is one of the first docking software that take full advantages of the multiprocessor hardware. Tested on two processor systems, ESCHER runs about 1.8 time faster than an equivalent single processor workstations (same CPU and same clock). These performances can be increased optimizing the code that was not originally developed to the parallel execution. ESCHER NG can run also on single processor systems in sequential mode. - Language localization. The Win32 version is included in the latest VEGA OpenGL package and in the full package we can find the source code and the executables for Win32, Irix6.2, Linux, AmigaOS. Best regards Giulio Vistoli and Alessandro Pedretti

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VEGA1.5.1 release
by Giulio Vistoli 17 Dec '03

17 Dec '03

Dear all, We are proud to announce the release of VEGA1.5.1 release that is freely downloadable at www.ddl.unimi.it. Among the several new functions we would like to focus your attention on the capability to add the hydrogens, on the complete 3D molecular editor with fragment libraries and on the database engine. New features: - Chem3D loader. - Accelrys archive file (.arc) support in the trajectory analysis. - Capability to add the hydrogens. - RMSD calculation in the trajectory analysis. - CHARMM lipid and GRID force field templates. - POPC lipid bilayer cluster in crystal and solid phase. New OpenGL features: - ESCHER NG and ESCHER NG Plugin: protein-protein and DNA-protein docking system. - Database engine for directory, sdf and zip files. - Complete 3D molecular editor with fragment libraries. - Multiple workspaces. - Remove residue/s dialog box. - Molecule place dialog box. - Fix/merge molecules. - Multiple Mini Editor and Graph Editor windows. - Now the centroids can be updated dynamically or kept fixed. - The residue renumbering is now available for all atoms and for the selected atoms only. Best regards Giulio Vistoli & Alessandro Pedretti

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Molecule of the Month - december
by Paul May 01 Dec '03

01 Dec '03

Hi, December's MOTM is sulfur dioxide SO2, which is one of the major components of acid rain. It has been written by Mike Thompson from Uppingham School, and is available in all common formats. http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm#dec2003 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> Mobile: 07811371539 Home URL: <http://www.bris.ac.uk/Depts/Chemistry/staff/pwm.htm> Molecule of the Month: <http://www.bristol.ac.uk/Depts/Chemistry/MOTM/motm.htm> Bumper sticker: "Where are we going? And why are we in this hand-basket?" ------------------------------------------------------------------------------

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CML viewers
by Eugen Leitl 19 Nov '03

19 Nov '03

What's a good current free viewer for CML structures embedded in HTML, if we're looking at 2D-Structures only? Right now I'm lookinig at JChemPaint; I wonder whether there are any recent projects I'm overlooking. Thanks! -- Eugen* Leitl <a href="http://leitl.org">leitl</a> ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE

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