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Early on, chemists were using the Internet much as anyone else: some e-mail, a few discussion groups, software exchange and the like, accessing library catalogues, developing their own simple home pages, eventually listing personal favourite sites, accessing lists of journals information and so on. Gradually though research groups started providing more and more detail about their work, whole departmental prospectuses began to appear online and the more forward-looking publishers began to provide easy access to some parts of their journals on the Web without the need for major database investment.
When German research chemist Rolf Claessen was a student at the University of Würzburg he began to build up a collection of links to these growing chemistry resources. There are probably thousands of links on his site (now called Claessen.net) which is indicative of just how quickly the Internet changes. When I first visited his student site some years ago, he probably had no more than a hundred or so links. Now, through well-maintained sites such as this and others in the chemistry departments of UCLA, Sheffield, Liverpool and elsewhere, chemists can access the web pages of colleagues in academia and industry, track down chemistry software – both commercial and public domain, find a route to a patent searching site, subscribe to and search a database and much more.
One overriding factor that has gradually emerged as the Internet has developed, however, is that the sense of community that chemists involved in front-line work – attending conferences and symposia, publishing and refereeing journals, working at the bench and all the other facets of scientific life – have not been lost. There has been a fear among some sectors of society that the Internet would lead to a numbing of human contact. Admittedly, you may not be able to have a face to face discussion with a colleague on the other side of the world but the development of highly popular discussion groups, such as chemweb – all lower case this time – provide new contacts that might only have been made at the occasional visit to a society congress, or whatever. If anything, we have more human contact than ever before through the global connections now in place.
Indeed, the development of online communities has surged. For instance, ChemWeb rode in on the electronic wave initiated by its older biomedical sibling BioMedNet. Launched in April 1997 by the Current Science Group in collaboration with software house MDL Information Systems, its banner proclaims it to be the ‘The World Wide Club for the Chemical Community’. ChemWeb’s membership has gradually increased to well over 160,000 in just two and a half years. One might even compare this figure with the rather less voluminous memberships of even national chemistry organisations such as the Royal Society of Chemistry.
ChemWeb.comAs ChemWeb becomes increasingly well recognised as a global chemistry community then the national and often parochial memberships of the ‘learned’ societies may at some point lose certain aspects of their appeal altogether. One might cynically suggest that members of any of these virtual communities might be rather transient, as is the fickle nature of the average Web surfer, but browser statistics demonstrate this is not the case. Most members join and keep coming back to reap the benefits, and are, in a sense, even more active than most members of the old-style learned societies. There may even be greater incentive to remain loyal to a virtual community because membership numbers are so high meaning diversity can be greater.
The learned societies have not left their positions wide open. The American Chemical Society, for instance, has developed ChemCenter which aims to provide its members and any chemist who cares to register with access to the online resources of the ACS and beyond. The Royal Society of Chemistry on the other hand has pooled its resources with those of other national chemical societies to create ‘chemsoc’.
ChemsocWithin the industrial chemical world, ChemConnect’s World Chemical Exchange was created to satisfy chemical industry demands for access to materials through a single interface. Rather than having to trawl through company catalogues to find a supplier, members of this community can buy products with a few mouse clicks. There are some 10,000 regular users from traders, manufacturers, and distributors to the end user in industry.
ChemConnectWhile the underlying aims of these different organisations are perhaps commercially distinct their overriding principle is to create community through the use of cyberspace. In fact, as distinct as they seem at the superficial level, the nature of the Internet means that collaborative links and resources are plentiful with each site generally providing some complementary links and information to the others and at the least they are working towards a common goal. The end user – chemists – should ultimately, in principle at least, find access to the information they need transparently and their allegiance to the science rather than individual organisations remain untouched by the profound changes taking place in the world of communication.
Virtuality is not likely to replace personal contact totally (I hope) and chemists will continue to attend conferences and chat in the coffee room…at least until the last molecule has been studied! But, given limited financial resources, online communities will provide individual chemists with the opportunity to handshake electronically with many more colleagues than is possible in a whole career of conferences.
- http://www.chemsoc.org/ – United European chemical societies
- http://www.chemcenter.org/ – ACS chemistry resources
- http://www.chemweb.com/ – online community
- https://exchange.chemconnect.com/ – ChemConnect chemical industry exchange
- http://sci.mond.org/ The Society of Chemical Industry
- http://www.claessen.net/ Rolf Claessen’s chemical links database
- http://www.lists.ic.ac.uk/hypermail/chemweb the chemweb discussion group
The CSA’s web site, of course, can be found at http://www.chem-structure.org/ and as you know the organisation aims to create its own community through which members involved in handling chemical structure information can work together.
David Bradley is a freelance science writer based in Cambridge, he can be contacted through his Elemental Discoveries site at SCIENCEbase.com
The new Michael Lynch laboratory Several of Mike Lynch’s former colleagues and students gathered at the University of Sheffield in December to witness the official opening of the newly refurbished computer lab for the Computational Information Systems Research Group in the Department of Information Studies, which has been named in his honour. The refurbishment of the Michael Lynch Laboratory has been paid for by a grant from the Royal Society, using funds from the Wolfson Foundation, and the opening was attended by Professor Eric Ash (Treasurer of the Royal Society), as well as by Professor Gareth Roberts, Vice-Chancellor of Sheffield University.
Professor Sir Gareth Roberts, Professor Sir Eric Ash, Professor Mike Lynch and Professor Peter Willett at the opening of the Michael Lynch laboratory
From the early 1960s Mike Lynch was a pioneer of research in the field now known variously as chemical informatics, cheminformatics, chemoinformatics or chemiinformatics, and many members of the CSA studied under his guidance during his tenure at Sheffield University. The new air-conditioned laboratory, which is equipped with seats for 20, along with a good selection of PCs and workstations, is a fitting tribute to Mike’s pioneering work. It is certainly a far cry from the tiny box-room with one dumb terminal, which was the extent of the Department’s computing facilities when I was one of his students!
At the ceremony, introductory remarks were made by Professor Peter Willett, who directs the research group (and has recently succeeded Mike as Honorary President of the CSA) and by Professor Roberts. Sir Eric then invited Mike to unveil the plaque, after which current members of the research group chatted with the guests, and demonstrated some of the computer systems on which they are working.
Ian Bruno wins the Ernie Hyde Award 14 members turned up for the AGM on 6th December at the Linnaen Society, London, when we welcomed 2 new members of the Executive Committee, John Holliday from the Department of Information Studies, Sheffield, and Bryan Vickery from ChemWeb. Thanks were given to Ian Bruno who retired from the Committee after many years of service. Ian has contributed a great deal to the work of the CSA, particularly by helping with the Chemistry and the Internet workshop held in Sheffield in 1997 and by setting up an Executive Committee listserver enabling us to meet electronically. In recognition of his outstanding contribution, Ian received the 1999 Ernie Hyde award. Unfortunately, Ian was unable to attend the AGM, but the photo shows Ian receiving the award in a pub in Cambridge.
Ian Bruno with his Certificate
The Tai Chow Mien Noodle Bar at the Elephant and Castle (£2.75 for all you can eat) was booked solid, so the CSA annual dinner returned on 6th December last to the esteemed Cadogan Hotel, after a one-year diversion to the nearly Basil Street Hotel. In my opinion, the Cadogan has the edge in ambience and food, and we are fortunate that Janet Ash has an inside-track family contact for making the booking, and (who knows?), maybe getting just the teeniest degree of superior attention in our private dining room. As one anonymous guest was heard to remark, “If it was good enough for Oscar Wilde to get arrested in, it’s good enough for me”!
So many turned up (18) that the staff had to bring in a connection table to make more seating space. (Groan, yes I know I’ve used that joke before, but I did invent it. It has now been assigned to the error file of history). A number of Trustees of the CSA Trust from far-flung parts of the world had made the effort to come. For me, there were a few unfamiliar faces and my only mini-complaint was that there wasn’t enough time before dinner to meet everyone, and most people are inevitably seated too far away to make conversation with. However, the meal was again excellent. What an accumulation of intellect under one roof; Jane Macintyre seems to become cleverer the further she gets away from chemistry. There must be a moral there; I’m reminded of the old joke about the Scotsman who moved to England and raised the average IQ of both countries.
Many thanks, Janet, for arranging this again, and I’m delighted that it can be continued for the year 2000. And no, Peter Nichols didn’t get arrested.
PLEASE NOTE: If you missed the dinner in December, the year 2000 annual dinner will be back at the Cadogan in the evening of December 4th, before the start of the Online meeting. Make a note in your diary now!
Gmelin Database Revived On December 6th 1999 the future of the Gmelin Database was decided with the Gesellschaft Deutscher Chemiker (GDCh) and Elsevier Science / BeilsteinInformationssysteme GmbH (BIS) / MDL Information Systems Inc. as details were finalised for an exclusive license agreement. This will ensure the continued rights for the distribution and sales of Gmelin but additionally provide full production rights including all future updates. The investment and commitment required to restore and develop the Gmelin Database will be made as soon as the final approval of the Bundesministerium für Bildung und Forschung (BMBF) is received.
This is seen as a significant break through and important in securing the synergy between BIS’s existing products and synonymous with the companies values for providing the customer with valuable, in-depth data coverage for the scientific community. This will also further enhance the product suite provided by Elsevier Science, reinforcing the link between primary literature from ScienceDirect to the high quality scientific details excerpted for Gmelin.
The essence of the final negotiations has been an exclusive license agreement, which has been granted by the GDCh who will play an important role with BIS. Together we aim to restore Gmelin’s status, as the worlds most comprehensive Database for Inorganic and Organometallic compounds which in 1994 held 1.3 million compounds. The GDCh has recognised the need to fill the data gap of 1995 to 1999 and has committed to do so, within only a four-year period. In an effort to remain focused on the scientific community’s needs the GDCh has pledged to provide support via an advisory board which we see as an invaluable contribution.
GDCh/BIS must also take this opportunity to thank all the parties especially the Max Planck Gesellschaft (MPG) for their constructive contribution in the previous discussions leading to a positive result.
Most importantly the real driving force behind our determination to come to an agreement was the encouragement received from our customers. We now hope with this new agreement and with the support of our customers, we can take Gmelin into the Millennium.
JChemPaint – help required JChemPaint is a Java 2 program for drawing 2D chemical structures like those found in most chemistry textbooks. Its GUI is based on the Swing tool kit. The program is developed as an Open Source Project and released under GNU General Public License. The code should be considered alpha quality, but there are enough features implemented to get an idea about where the program development is heading.
JChemPaint development is coordinated by Christoph Steinbeck and his Chemical Information group (http://www.ice.mpg.de/departments/ChemInf) at the Max Planck Instiutute of Chemical Ecology (http://www.ice.mpg.de/).
Version 0.5 now features:
- A subset of the regular drawing features of commercial programs, as there are
- drawing of single, double, triple and stereo bonds.
- stereo bonds
- deletion of bonds and atoms
- ring templates (3-8)
- one-click attachment of ring templates to an atom or a bond
- flipping and rotating selected parts of the molecule
- Loading and saving of structures in Chemical Markup Language (CML) and as MDL Molfiles.
- Automated Structure Layout, also known as Structure Diagram Generation.
- Loading structures over the Internet from the “Dictionary of Organic Chemistry” (http://www.sci.kun.nl/woc/) using the CAS number.
More information as well as a download option can be found on http://www.ice.mpg.de/~stein/projects/JChemPaint/
People are sought to join the development of JChemPaint. JChemPaint is associated with the OpenScience project (www.openscience.org) and the 3D molecular viewer JMol (http://www.openscience.org/jmol/), both initiated by Dan Gezelter at Columbia University (http://www.chem.columbia.edu/~gezelter/).
ADMINISTRATION The new CSA Executive Committee Click here to see a list of the new Executive Committee.
Have you paid your subscription? Requests for payment of membership dues have been sent out by e-mail this year, where we have an e-mail address for you. If you have not received the request, please contact Gez Cross on email@example.com. To continue receiving Newsletters and the password to the latest Newsletter on the web, please pay as soon as possible.
If there are several CSA members in your company, you may prefer to send one cheque to cover all the members, but please nominate one person to send us a list of all the individual members. Don’t forget to include any details specific to the individual members (e.g. phone numbers, faxes etc.) and especially their e-mail addresses, too. A special multi-member form is available on request from Gez, if required.
MEETINGS Joint CSA/CINF Symposium on Chemical Information and E-Commerce A special joint session of the American Chemical Society’s (ACS) Chemical Information Division (CINF) and the CSA will take place on Tuesday 28th March 2000.
The Joint CSA/CINF Symposium, entitled “Chemical Information and E-Commerce” is a full day session forming part of the 219th National Meeting of the ACS, 26 – 30 March 2000 – San Francisco, California. The session will be chaired by Bryan Vickery, Community Development Manager, ChemWeb.com [http://chemweb.com/].
The call for abstracts was met with enthusiasm by all chemical e-commerce platforms operating today, and even by some about to launch. Recent articles in Chemical & Engineering News (C&EN, 12 July 1999, 11-18) have highlighted the explosion in the area of e-commerce in the chemicals industry – which includes retail (books, software) and business- to-business (b2b) platforms.
Titles, speakers and organisations are listed here:
- Integration of technical information with on-line buying increases the chemical procurement efficiency John Custer, Internet Strategies, Sigma-Aldrich Research [http://www.sigma-aldrich.com/]
- Demand aggregation in real-time as a new model for e-commerce Lane S. Yago, PowerPurchasing Group [http://www.powerpurchasing.com/]
- Bringing clarity to e-commerce in the industry Brad Lich, Vice President of Marketing, e-Chemicals Inc [http://www.e-chemicals.com/]
- Chemical information and e-commerce in the 21st century: The role of the infomediary in online commodities trading Arlyn R Sibille, Vice President Analytical Testing, WorldWideTesting.com [http://worldwidetesting.com/]
- Integrating reagent selection, ordering and inventory management Charles D. Sullivan, Maurizio Bronzetti, and David A. Evans. MDL Information Systems, Inc [http://www.mdli.com/]
- Leveraging e-procurement in pharmaceutical R&D Mark Robillard, Vice President of Electronic Commerce, EMAX Solution Partners [http://www.emax.com/]
- E-commerce models: changing the way vertical industries do business Kevin Wenta, CheMatch [http://www.chematch.com/]
- Proven Benefits of e-commerce for chemical buyers and sellers John Beasley, ChemConnect [http://www.chemconnect.com/]
The session will be concluded by a panel discussion: Online marketplaces: Strategies for reaching customers through electronic commerce to include many of the speakers and David A. Weber, Supplier Relations, Chemdex [http://www.chemdex.com/]
AWARDS AVAILABLE CSA Trust Year 2000 Award The Chemical Structure Association Trust is an internationally recognised Trust established to promote education, research or development in the area of systems and methods for the storage, processing and retrieval of information about chemical structures, reactions and compounds.
Applications are invited for the Year 2000 Chemical Structure Association Trust Award. The Trust is offering an Award of up to two thousand pounds sterling for the best applicant seeking funds for education or research in chemical information.
Anyone working in the field of chemical information research can apply and application can be made for funds to attend a relevant conference, for travel (e.g. to collaborate with another research group) or for hardware or software to assist with the research project. The award is unlikely to be given exclusively for hardware and software. The application should include:
- A statement of academic qualifications
- Details of relevant work and a statement of research recently completed by the applicant
- The purpose for which the award is required. The clarity and relevance of this statement will be crucial in the evaluation of the applicants
- Letters from two academic references to support the application.
Award winners are expected to write a short report, within one year of receiving the money, giving details of how the money was spent.
The Trust has previously supported the continuation of research studies in biomedical interactions including molecular recognition processes and drug design; a novel combination of reaction indexing and synthesis planning; clustering of chemical structures for property prediction; and investigation of reaction mechanisms. The work of younger scientists in developing countries has also been made possible in conjunction with some of the awards.
Recent award winners, and their areas of research, are as follows:
- Marina Molchanova, Zelinsky Institute of Organic Chemistry, Moscow (use graph theoretical and combinatorial algorithms in structure generation)
- Weifan Zheng, University of North Carolina (QSAR and combinatorial chemistry)
- Aniko Simon, University of Leeds (chemical literature data extraction)
- Eugene Babaev, Moscow State University (computer-assisted synthesis)
- Gareth Jones, University of Sheffield (for presentation of paper on genetic algorithms at an ACS National Meeting)
- Vladimir Kvasnicka, Slovak Technical University (neural networks for prediction of physiochemical properties)
- Rainer Herges, University of Erlangen-Nuernberg (reaction databases and quantum chemistry)
Applications must be submitted by 30 April 2000, preferably by e-mail, to the Chairman of the Awards sub-committee, Professor Michael Lynch, at: M.Lynch@sheffield.ac.uk
Any postal applications should be sent to:
Dr Clive Weeks
Secretary of the Chemical Structure Association Trust
39 Rounton Road
Fleet, Hants GU13 0JH
The Award will be presented at the International Chemical Information Meeting in Annecy in October.
AMERICAN SOCIETY FOR INFORMATION SCIENCE (ASIS) ANNUAL MEETING 2000The ASIS Special Interest Group/Scientific and Technical Information Systems, through a grant from Chemical Abstracts Service, a division of the American Chemical Society, is offering from $500 to $1,000 to defray the cost of attending the ASIS annual meeting:
Knowledge Innovations: Celebrating Our Heritage, Designing Our Future Chicago, Illinois, November 13-16, 2000.
Information on the meeting can be found at http://www.asis.org/
- A demonstrated interest in chemistry and information science by a current graduate student. Full-time enrolment is not mandatory, but will be given strong preference.
- Completion and submission of the application form at http://www.asis.org/SIG/SIGSTI/
For more information, please contact:
Dr. Jian Qin, Awards Chair, SIG/STI: (315) 443-5642; (315) 443-5806 [fax] firstname.lastname@example.org
DEADLINE: MARCH 15, 2000
Applicants will be notified of results by April 30, 2000
DESCRIPTION: The scholarship is designed to help persons with an interest in the field of Chemical Information to pursue graduate study in Library, Information or Computer Science.
CRITERIA: To be eligible, one must have an undergraduate degree with a major in Chemistry, and have been accepted into a graduate program in Library, Information or Computer Science. Work experience in Library, Information or Computer Science preferred
TO APPLY, SEND THE FOLLOWING ITEMS TO THE ADDRESS BELOW:
- Letter of application giving the reasons you should be considered for the award
- Transcript of undergraduate studies
- Three letters of reference
- GRE scores (this item is optional)
DEADLINE FOR APPLICATIONS: March 17, 2000
Division of Chemical Information
145 Raven St.
Iowa City IA 52245
Phone: 319-335-3085 (daytime only)
BOOKS AND JOURNALS Special subscription offer for Journal of Computer-Aided Molecular Design Journal of Computer-Aided Molecular Design is an international journal which publishes 8 issues per volume year. The journal provides a forum for disseminating information on both theory and the application of computer-based methods in the analysis and design of molecules. The journal publishes papers which report new and original research and applications in areas such as theoretical and computational chemistry, computer and molecular graphics, molecular modelling, protein engineering and drug Dr. Gerhard Klebe (Phillips University of Marburg, Germany)
- Dr. Andrew Leach (Glaxo Wellcome Medicines Research Centre, U.K.)
Kluwer is delighted to offer the members of the Chemical Structure Association a special subscription rate of US$150 for Volume 14 (2000, 8 issues) together with the journal Perspectives in Drug Discovery and Design (3 vols). Please send a completed subscription form (below) to:
Kluwer Academic Publishers
Order Department – Journals
P.O. Box 322
3300 AH Dordrecht
Fax: +31 78 6546474
Yes, I am a member of the Chemical Structure Association and I would like to obtain an individual subscription to the Journal of Computer-Aided Molecular Design (Vol. 14) together with the journal Perspectives in Drug Discovery and Design (Vols. 18/19/20).
First book on Pharmacophores The first book on Pharmacophores has been released: “Pharmacophore Perception, Development, and Use in Drug Design,” Edited by Osman F. Güner. Illustrated, hardcover, $109.95, 560 p. Color ill. (IUL Biotechnology series), ISBN: 0- 9636817-6-1, 2000 (see http://www.iul-press.com/)
Perceiving a pharmacophore is the most important first step towards understanding the interaction between a receptor and a ligand. Here is the closing paragraph from the Preface:
“In closing, consider the history of aviation with the very first flight taking place in the early 1900s and, the moon landing a mere 50 years later. Contrast this to the first use of the term “pharmacophore.” It was first used in early 1900s as Peter Gund explains in Chapter 1; however, the meaning of the definition remained remarkably unperturbed during its close to 90 years of existence. Today, a pharmacophore is considered one of the most important types of “information” that can be obtained from a receptor-ligand interaction. Pharmacophore is the key to discovery and design of new leads. Yet, quite surprisingly, this book is the first book that is dedicated to pharmacophores in drug design . We therefore wanted to be very comprehensive in this first volume, covering all aspects of pharmacophore perception, development, and use in drug design. We hope that you will find this book useful to bring your computer-aided drug design endeavor to a higher level.
Osman F. Güner”
This is what Prof. Robert S. Pearlman commented about the book: “Computer-assisted drug discovery (CADD) has been and continues to be an essential component of competitive pharmaceutical and agrochemical discovery programs. In many respects, pharmacophore perception and the use of perceived pharmacophores comprise the fundamental essence of all CADD methods. Rather than reducing the need for CADD methodology, recent advances in combinatorial chemistry and high- throughput screening have accentuated the importance of CADD techniques for lead exploration and lead optimization while simultaneously providing more data and new challenges for pharmacophore perception algorithms and related applications. This unique volume, focused on pharmacophore perception and applications, could not have been published at a more opportune time and the Editor has ensured that it will appeal to a very broad audience. His own Introduction coupled with chapters by the pioneers in pharmacophore perception provide a clear perspective which enables both newcomers and experts to appreciate the state-of-the-art perception methods described in subsequent chapters. He has also included chapters discussing applications ranging from qualitative methods such as 3D-searching and other forms of database mining to quantitative methods such as CoMFA and receptor-ligand docking scores. The two sections on analog-based and receptor-based pharmacophores correspond to the two fundamental approaches to computer-assisted drug discovery: ligand-based and receptor-based design. By compiling chapters discussing the background, current methods, and a prospective discussion of future directions, the Editor has ensured that this book will be a valuable resource in both the research lab and the classroom, now and for years to come.”
Robert S. Pearlman, Ph.D Chair in Pharmacy and Director, Laboratory for Molecular Graphics and Theoretical Modeling, College of Pharmacy,University of Texas
The book is available through Internet (Amazon.com, Barnesandnoble.com) as well as through bookstores.
PRODUCT NEWS ACD ACD/I-Lab II Online Prediction and Database Service from Advanced Chemistry DevelopmentWith a list of services including systematic naming generation, NMR and physicochemical prediction, and online database searching by structure and substructure, the Interactive Laboratory (I-Lab) has become renowned as the one-stop shopping mall for prediction capability. The first release of I-Lab saw a Java-based site offering a structure drawing applet and Molfile upload to initate prediction and searches. In 1999 Advanced Chemistry Development released I-Lab support for ACD/ChemSketch, the FREE PC-based structure drawing package. As a result we have performed over 50,000 predictions and database searches in the last six months. Now we are proud to announce the release of I-Lab II, the commercial venture. With added capability in terms of both prediction technologies and databases I-Lab II offers access to our industry standard tools via an internet connection. It is possible to pay-per-prediction or to subscribe to one of more services for a defined period of time. There are already academic schools taking advantage of annual site licences! I-Lab II will surely be recognized again as the portal to one-stop shopping for predictions and property database searches. Visit us now at http://www2.acdlabs.com/ilab and sign up for your FREE trial.
CambridgeSoft ChemOffice WebServer 2000 is now available. It is the only out-of-the-box enterprise solution for finding and purchasing research chemicals! ChemOffice WebServer connects to industry standard data sources, such as MS SQL Server and Oracle, and serves and searches chemical data.
New 2000 enhancements include saving queries, marking hits, increased control over result displays, and integration with ChemFinder for Excel. Results, including chemical information, from WebServer searches can be exported directly into Excel or exported and loaded into a local ChemFinder DB for management of project data. ChemACX-SC adds a robust database of screening compounds to the ChemACX offerings. The built-in ChemACX application contains triple the vendors, over 500,000 products, and can be integrated with existing purchasing systems, or serve as its own!
Other new applications in WebServer 2000 are a two-tiered Chemical Registration, complete with batch management, automated duplicate checking, and physical data management. Also available are applications for serving Derwent data (such as World Drug Alerts), ISI reaction databases (such as the CCR), and reaction databases from InfoChem GmBH.
ChemOffice WebServer is used throughout the chemical industry, from small laboratories and groups to large Fortune-100 enterprises. Its value and scalability makes it the only choice for chemical information needs. Now, ChemOffice Webserver comes in Ultra and Pro versions.
CAS Registry Enhanced with More Biosequence Data CAS is now assigning CAS Registry Numbers to all sequences in patents, and is placing additional valuable information in the CN field, including the patent number and the location of the sequence information in the patent (SEQ ID or Figure Table or Page Number).
Biosequences continue to grow as a component of CAS databases. In 1999, more than 2.8 million sequences were added to the CAS Registry, representing nearly 80% of all registrations for the year.
To learn more about this and other enhancements to CAS files, visit the web site at http://www.cas.org/STNEWS/stnewscover.html.
CCDC The April 2000 release of CCDC’s Cambridge Structural Database (CSD) System, the repository of organic and metal-organic small molecule crystal structures, contains nearly 220,000 entries, but its most significant feature is the first release of ConQuest, the new face of the CSD. Designed to be much more user-friendly than the older QUEST database search program, ConQuest is supported on the PC Windows platform as well as UNIX and Linux. Construction of database queries and management of results is more straightforward, and search speeds have been improved. ConQuest therefore represents a huge step forward in making the vital resource of information contained within crystal structures available to researchers. ConQuest will be shipped to all CSD subscribers with their April release.
Also available from CCDC for the first time in April 2000 is SuperStar. This applications program directly uses information on intermolecular interactions extracted from the CSD to predict how and where organic functional groups will prefer to be located inside protein binding sites – an important step in understanding binding mechanisms or in ab initio ligand design. SuperStar is available to all CSD users as a paid add-on to their subscriptions.
For further information about the CSD System, ConQuest or SuperStar, please contact the CCDC at email@example.com, by phone at +44 1223 336408, or by post at 12 Union Road, Cambridge CB2 1EZ, UK, or consult our website at http://www.ccdc.cam.ac.uk/.
New members are now joining at the rate of around 11,500 a month, and page impressions now exceed 1 million a month. This represents a two and a half fold increase over this time last year. The September launch of Beilstein Abstracts free of charge to ChemWeb.com members had a dramatic impact on membership, as well as on traffic.
ChemWeb.com are trying to reach new deals with other content suppliers in order to increase the amount of free information available to its members on the site. At theOnline meeting in London in December, ChemWeb.com announced the launch of twelve Marcel Dekker chemistry and physics online journals. The journals are available on a personal online subscription basis. Searching, tables of contents and abstracts are free. Also going live on the site was Johnson Matthey PLC’s journal Platinum Metals Review. The journal is available to ChemWeb.com members free of charge.
Synopsys Scientific Systems Ltd. has announced the release of version 3.1 of its Accord Software Development Kit (SDK) on a full range of client and server platforms, including Windows 95/98, Windows NT, SUN Solaris, SGI IRIX and RedHat LINUX. The Accord SDK is a chemistry toolkit that allows in-house developers to harness the full power and chemical sophistication of the Accord Chemistry Engine in developing their own client or server-based applications. This release of the Accord SDK is the first to be made generally available on UNIX & LINUX servers and is the first chemical software to offer equivalent toolkit functionality on the desktop and server.
This new, improved version of the Accord SDK provides full support for query features, stereochemistry, organometallics, delocalised pi-systems, polymer repeating units, stoichiometry, and a host of other chemical representation enhancements. In addition, the Accord SDK Chemistry Object Model has been extended to provide full access at the atom and bond level to facilities such as substructure matching, colouring and entity set manipulation. This vintage release of the Accord SDK, for the first time, allows both client and server chemical applications to be developed on top of one underlying chemical representation framework. This symmetry means Accord- based components and business objects developed by customers can be deployed on the client, the middle tier or database server as required.
The Accord SDK is fully reentrant and its toolkit functions are callable from the macro and scripting languages of mainstream software packages, such as Microsoft Office and Oracle. Stand-alone applications can also be developed using Visual Basic, Delphi or C/C++. The Accord SDK provides the ideal building blocks from which sophisticated chemical solutions can be developed in record time. In-house developers can rely on the Accord SDK to provide the underlying chemical framework on which they can base their application solutions.
Because Accord allows industry-standard development tools and ‘containers’ to be used in developing chemical applications, programmer productivity is increased and Microsoft and Oracle skills come to the fore. Numerous sample applications, along with source code, are provided as part of the Accord SDK. In-house developers are encouraged to use these as the basis for their own applications. Indeed, Synopsys itself uses the Accord SDK to develop end-user solutions, such as its Accord for Microsoft Excel chemical spreadsheet product. Users of all products in the Accord range can leverage the Accord SDK to perform complex tasks or implement chemical algorithms. For example, Accord for Oracle provides interfaces to allow Accord SDK functions to be called within Oracle PL/SQL functions, which might be used to create triggers that implement chemical business rules. In addition, the Accord ActiveX Chemistry Control is the ideal complement to the Accord SDK, providing chemical visualisation and desktop integration via the Web and other client-side user interface development tools, including Visual Basic and Delphi.
Accord for Excel 2000 and Accord for Access – Office 2000 compatible
Synopsys has also released a Microsoft Office2000 compatible version of Accord for Excel, the world’s first desktop chemical spreadsheet solution, and Accord for Access, its best-selling desktop chemical/relational database system. These new, improved versions provide full compatibility with the latest Microsoft Office2000 release, allowing users to take advantage of the new features in Access2000 and Excel2000, including Extensible Markup Language (XML) and ActiveX Data Objects (ADO) support.
Accord for Access2000 provides full support for storing and searching chemical structure and reaction information directly within an industry-standard SQL framework. In essence, Accord makes chemistry a first-class datatype, on a par with numbers and text, within Access, the world’s favourite, desktop, relational database environment. The Accord approach removes the limitations imposed by proprietary flat-file and hierarchical databases, allowing the power of the relational model to be applied to chemical problems.
Accord for Excel provides scientists with a full range of chemical facilities to manage, analyse and search Accord chemical ‘objects’ and associated data directly within the spreadsheet. Only with Accord for Excel can users insert chemical structures, reactions and substituents directly into spreadsheet cells with retained chemical awareness. This unique feature of the software allows chemically-meaningful functions to be linked to chemical cells for calculating derived properties, such as molecular weight, percentage composition or LogP. In addition, operations on chemical tables, su ch as R-group analysis and substructure filtering, can be performed directly within Excel.
Both Accord for Access2000 and Accord for Excel2000 work seamlessly together and are two key components of the Accord Desktop Product Range. Datasets of interest can be transferred from Accord for Access2000 to Accord for Excel2000 at the push of a button. Data can also be imported and exported in a variety of formats including MDL SD and RD files. Accord for Access2000 can also act as a client to access Accord for Oracle chemistry tables via ODBC to create applications as diverse as chemical registration, data warehousing and sample tracking.
Accord for Excel and Accord for Access can be used out-of-the-box, but also provide the ideal building blocks from which sophisticated chemical solutions can be developed in record time. In-house developers can rely on Accord to provide the underlying chemical framework on which they can base their application solutions. Because Accord allows industry-standard development tools and ‘containers’ to be used in developing chemical applications, programmer productivity is increased and Microsoft skills come to the fore. Numerous sample applications, along with source code, are provided as part of the Office2000 compatible releases of Accord
Synopsys announced a new release of its popular Metabolism database, significantly increasing the coverage of agrochemical data.
Synopsys’ approach to the development of its Metabolism database has been to collaborate with expert groups, with the aim of providing a high quality product, relevant to the information needs of researchers within the pharmaceutical, agrochemical and fine chemical industry. Forming a firm foundation for the database have been two, well-respected reference works: Biotransformations (ed. David Hawkins) and Metabolic Products of Agrochemicals (ed. Terry Roberts), published in the UK by the Royal Society of Chemistry; the bulk of this new release is derived from this latter work.
The design of the product, essentially as a reaction database, whereby the test compound is the reactant and the metabolite the product, allows structural and related data to be searched within familiar, industry-standard chemical search software, such as ISIS and Accord. Judicious use of the database enables scientists to better understand and predict the likely metabolic fate of new active compounds within biological systems, thereby influencing their development as early as possible in the discovery cycle.
The latest release of the Metabolism database (version 99.1) comprises 15,000 transformations, representing over 2,000 test compounds and more than 3,000 literature citations. The database will grow by an estimated 10,000 transformations per year during 2000 and 2001; thereafter, six-monthly maintenance releases will keep the database up to date with approximately 1,500 new transformations annually.
PERSONALIA We are sorry to say goodbye to Jos Porskamp. Previously, Jos was information officer and Quality Assurance Manage for Akzo Nobel Central Research. From the first of November, Jos became Manager General Affairs of Akzo Nobel Chemicals Research Arnhem with responsibility for Services & Facilities, Quality, Health & Safety. Jos says “During the past years your newsletter was of great interest for me and I like to thank the CSA for helping me in performing my former job.” We wish him all the best in his new position.
Daniel Keesman is now Vice President and General Manager, MDL Europe. His predecessor, Hansruedi Kottman, has joined Base4 as Vice President of market development. In his new role, Hansruedi will support Base4’s continued growth in global, pharmaceutical accounts.
Jason Theodosiou has been appointed Vice President and general manager of European systems with EMAX Solution Partners, Inc., after spending 12 years at MDL Information Systems.
Tad Hurst, Scott Hunton and Robert Feinstein are now running ChemNavigator.com Inc., a new San Diego-based e-commerce company serving the life sciences research community.