Issue 52

Newsletter

Issue 52

July 1999

NOTIFICATION of CSA AGM and DINNER The 1999 CSA AGM and Dinner will be held on Monday 6th December (the Monday of Online week).

The AGM will be at 4.00pm at the Linnean Society, Burlington House, Piccadilly, London. The agenda will be published in the next Newsletter.

The Dinner will be at 7.00 for 7.30 pm, by popular request back at the Cadogan Hotel, Sloane Street. To book, please contact Janet Ash, ash@euronet.nl.

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REPORTS AND ARTICLES217th American Chemical Society Meeting, Anaheim Report by Fergus Lippi*

The American Chemical Society (ACS) meeting was held in Anaheim, California (USA), from the 21st to 25th of March 1999 at the Anaheim Convention Centre. The ACS is a self-governed individual membership organization that consists of over 151,000 members—60% from industry, at all degree levels. There are 34 ACS divisions, representing a wide range of disciplines for chemists, chemical engineers and technicians. Each division was represented at the national meeting and each held an individual symposium. The number of attendees was approximately 12,000 and the exposition booth in the convention centre represented about 400 companies and universities.

Sunday the 21st of March was the official start of the meeting. In the morning I attended David Wilde’s speech on “VisualisSAR” (Division of Chemical Information (CINF) session) as he was using similar methods to the ones I am working with during my research. The speech focused on the use of modal fingerprints to isolate features in compounds that would enable the user to perform a focused database search. Since I have been working with binary strings upon which modal fingerprints are based, this speech proved to be very interesting. Modal fingerprints isolate the interesting features of a group of actives (the activity is known) by “and-ing” their respective chemical fingerprints. The result is a modal chemical fingerprint, which can be used as an “activity” identifier for molecules whose activity is unknown but for whom the chemical fingerprints are available.

As I am particularly interested in the use of Computers in Chemistry, I spent the rest of the time at this symposium attending the COMP session.

From Sunday to Tuesday, the symposium was entitled “Computational intelligence and data mining in high-throughput screening: Dirty QSar” (the morning had been spent in the CINF session attending David Wilde’s speech). The first speech of the Sunday afternoon session was by Peter Gund, from Pharmacopoeia Inc, and focused on the design of large combinatorial libraries. According to Peter Gund, drug strategy oscillates between theoretical (structure based design) and empirical (natural products design) approaches. P. Gund showed that it was possible to create large libraries that obeys rational (empirical) rules but can be designed using random (theoretical) methods. At present, a typical Pharmacopoeia library contains between 10.000 and 100.000 compounds and uses the ECLIPS technology. The design criteria are based on diversity and the drug-likeness of the compounds.

The second speaker for the Sunday afternoon session was Keith Davies (Treweren consultants Ltd) and concentrated on the use of De Novo methods for High Throughput Screening (HTS). The methods described showed a significant improvement compared to conventional HTS data processing methods. However, the method did not take into consideration the HTS data distribution and synthetic feasibility of the compounds obtained, hence setting the milestones for future research. The last speaker for the day was Marcus Wagener who worked on decision trees to discriminate between drugs and non-drugs. Using a tree that penalised the misclassification of a drug, 93% of the drugs were rightly predicted.

Monday morning was the opening of the companies exposition in the convention centre; Jack Delany and Roger Sayle (Daylight CIS) collaborated with our group in Portsmouth by providing some of the algorithms used in the research project and consequently the poster. After a short meeting, the poster (to be presented that night at the sci-mix poster session) was agreed. The exposition booths enable attendants at the conference to view some of the latest technology in the chemical and more generally the scientific industry. Companies such as Silicon Graphics, Daylight and Tripos were represented. At each booth, a company member was giving either a group or individual session to advertise his company products.

The afternoon session started with Paul Labut’s speech about binary QSAR. Paul’s approach is that a set of molecules should not be divided into active and inactive but separated using a probability that each assumption is true (or false). The error probability takes into account that some measurements might be wrong. The algorithm could be applied to virtual screening (prioritize screening libraries by estimating the number of actives and search for virtual hits). Other applications could be De Novo design via HTS and focused combinatorial library design (use binary QSAR molecules as focusing agents). It is possible to use HTS data, both negative and positive and the method can be used on large datasets.

The last speech for the afternoon session was by John Elling from Bioreason. The objectives of his research are to apply data mining tools to drug discovery, focusing on HTS data. To achieve this goal, phylogenetic trees were used to put active compounds into structural classes in order to build a pharmacophore model and finally evaluate the model. Using MACCS like keys to describe the compounds, it is then possible using Kohonen clustering to locally organize compounds in neighborhood. Hotspots are identified and used to obtain the Maximum Common Substructure (MCS). The next step is to locate the active parts in the MCS and learn new keys from the hotspots. Not all new keys are accepted as they must be reflective of the neighborhood and preference is given to smaller keys. The strengths of Bioreason trees lie in the fact that they allow multiple class belonging and capture information for all families of actives. The trees also show the multiple routes from which a single family can be derived. However their purpose is not SAR analysis but to separate compounds into structural classes in order to learn from their structures.

Monday night was “sci-mix” poster session and our poster was scheduled in the chemical information (CINF) section. Entitled “Mixed text and structure searching of chemical databases”, it focused on building a consensus tool for searching databases of chemical compounds by using the Daylight chemical fingerprint representation of a molecule to which new binary encoding were appended. The new binary encoding are respectively the band coding developed at the Centre for Molecular Design in Portsmouth and the Hamming-Gray coding provided by Roger Sayle from Metaphorics (USA). This method was tested on the Scott dataset (75 compounds along 14 different activity classes along with four measured properties: LogP, molecular weight, rotatable bonds and molecular refractivity). The results showed that the use of the appended codes improved the hit retrieval rate. However a lot of work still need to be done to validate this method, especially applying it to a larger dataset.

Peter Shenkin (from the chemistry department of Columbia University) presented Tuesday morning’s first speech entitled “Statistical Analysis of Combinatorial Chemical Sequences” (SACCS). The approach in SACCS is to analyze only the label that appears at the active site, it performs a statistical analysis which characterize the active pool. Using replicate, entropy, frequency and free-energy analysis, this approach does not aim at library design but tries to tackle the difficulties that could arise from the differences that exist between real and idealized experiment notions. The SACCS analysis was tested on 154 compounds and unfortunately did not agree with the “true” simulation. However it showed a stochastic correlation between the different concentration of hosts. Shenkin concluded with the fact that there is still a lot of research to be carried out.

Finally, qSAR (q for qualitative as opposed to upper case Q for quantitative used in QSAR) was the subject of Robert Clark’s speech and concluded the morning session. qSAR uses high dimensional visualization process to improve the quality of the hit rates. The method proved to be successful but the most interesting remark was in the conclusion when it was said that there was probably as much to learn from the inactive compounds than the active ones. The answer to the question “are actives any more specific than inactives?” could be answered by studying the inactives as well. This is a theory that our group has tried to emphasize on in the course of our research.

The Tuesday afternoon session sounded exciting thanks to Hua Gao’s speech from Pharmacia and Upjohn. His aim is to investigate a clustering algorithm based on Principal Component Analysis (PCA) in order to identify a preferred set of molecular descriptors. Our own research focuses on the encoding of such descriptors and therefore I was expecting a lot from this particular speech. By using mathematical equations, Gao was able to assess the quality of the different cluster analysis obtained via different set of descriptors. 20 different sets of descriptors were tested on various datasets and the results showed that the SS keys gave the best results.

Tuesday was also the conclusion of the “dirty QSAR” part of the COMP session and a panel discussion took place. The views expressed by some of the chemists present were that there was a need to come back to methods that would undoubtedly be slower but would offer a better quality of compound selection. The role of “dirty QSAR”, however, is to provide faster solutions, the downfall is that the quality is not be as good as traditional methods. Nevertheless, it provides the chemist with fast information and a smaller amount of compounds on which they can then apply their own methods.

Combinatorial Chemistry was the topic for the last two days of the CINF session. The speech by Yvonne Martin on Wednesday morning highlighted the method by which Abbott laboratories make their compound selections through leveraging HTS results. Using sets of filters Abbott performs a “virtual screening” in order to select their compounds. Tested on the DIVERset (39695 compounds), their clustering algorithm was shown to give roughly the same results as a randomized clustering. This is may be due to the fact that the compounds were weakly active. The speech concluded on the fact that almost all benefits came from removing the junk, which tends to suggest that most judgement is involved in eliminating “unwanted compounds”. The research is still carried out at Abbott laboratories.

In his speech, R. Pearlman from the University of Texas emphasised on the dilemma of selecting compounds. One would wish to maximize design criteria and economical issues. There is a need to compromise between these two factors and that requires a Reactant-Biased / Product-biased technique. (RBPB approach). Earlier implementation of such a system yielded compromise deemed unsatisfactory by combinatorial chemist and a new algorithm was therefore needed. By generating reaction-scores from product-scores, it is possible to consider many candidate libraries representing different combinations of reactants and plate layouts. The user can in turn determine the number of libraries and types of layouts and then pick reactants from each library. Pearlman showed that this new technique allows the design of diverse and economically efficient databases.

Thursday morning session was dedicated to structure based approach of combinatorial libraries and the different speakers talked us through a variety of methods. John Van Drye (Pharmacia & Upjohn) focused on the design of targeted libraries and the need to use understanding of SAR to design new ones. The first step is to generate all candidate pharmacophores and rank them according to their selectivity. (i.e. according to the number of hits they give). The shrink-wrap method is then applied to infer the shape of the binding site; all molecules are superimposed using the pharmacophore (2D or 3D) and the surface of smallest volume, which encloses at least one conformer of each active, is computed. J.W. Liebeshutz (Proteus Molecular Design Ltd.) introduced a new approach that combined Combinatorial Chemistry and Structure to discover new hits. This approach was tested for novel serine protease inhibitors and proved a powerful lead-finding tool.

All in all, the week spent in the United States was beneficial. It allowed me to go to my first major conference and meet various and interesting people. Furthermore, I was able, coming from a mathematical background, to appreciate what the chemists really wished or desired from new IT procedures. This will obviously be useful when the time for submitting the thesis will be nearing.

I would like to thank the Chemical Structure Association Trust and the University of Portsmouth for the funding. I would also like to thank David Salt, Martyn Ford and Michael Lipkin at the University of Portsmouth, John Bradshaw at Glaxo Wellcome UK, Jack Delany and Dave Weininger at Daylight CIS and Roger Sayle at Metaphorics. This has been a great experience and gave me the opportunity to present my research in a world class conference for the first time.

* Fergus Lippi is a final year PhD student in biology at the Centre for Molecular Design part of the University of Portsmouth (UK) and he presented a poster entitled “Mixed text and structure searching of chemical databases” at the American Chemical Society meeting in the sci-mix poster session.

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5th International Conference on Chemical Structures, Noordwijkerhout, 6th-10th June 1999 The first conference on chemical structures to be held in Noordwijkerhout (on the Dutch coast) took place in 1973, but it was not to be repeated till 1987, when the first of the current series of triennial meetings took place. The series rapidly established itself as a “must” for anyone interested in the theory and practice of chemical structure handling, chemical information science, chemoinformatics (or whatever it is that we all do). This fifth conference in the series was sponsored by the Chemical Structure Association and the chemical information divisions (or equivalents) of the American, British, Dutch, German and Swiss Chemical Societies, and it attracted over 170 delegates from 17 countries. The conference included a total of 29 papers, 51 posters and eight product reviews, a software exhibition, and a full social programme that, taken with the excellent culinary and recreational facilities available at this international conference centre, provided a very full and satisfying five days.

Two of the sessions were given over to computational methods to support combinatorial chemistry programmes: one session on library design and one on diversity and QSAR analyses. Wendy Warr (“Trends in combinatorial chemistry”) introduced the first session with an overview of recent and current developments in both combinatorial chemistry and high-throughput screening, and she was followed by several papers that described systems that had been developed at companies such as CombiChem (Robert Stanton on “The design of maximum information libraries as a highly efficient tool for lead generation and evolution”), GlaxoWellcome (Gianpaolo Bravi on “Optimisation of 3D focussed libraries with PLUMS”), Molecular Simulations Inc. (Robert Brown on “Structure-based design of combinatorial libraries”) and Rhone-Poulenc Rorer (Stephen Pickett on “Enhancing hit-to-lead properties of diverse libraries”).

Several aspects of combinatorial chemistry were discussed. If combinatorial libraries are to be of practical use, they must contain compounds that are synthetically feasible and that exhibit an appropriate mix of physicochemical properties, as emphasised by Peter Johnson (“De novo design of synthetically accessible ligands”) and Eric Martin (“Sensitivity analysis and other improved tools for combinatorial library design and mixture representation”). Bob Clark (“High throughput and combinatorial qSAR”) and Dimitris Agrafiotis (“Advances in the design and visualisation of combinatorial libraries”) discussed methods for visualising the results of diversity analyses that have been carried out in high-dimensional spaces. Finally, a range of new algorithms and data structures for processing chemical structure databases (whether real or virtual) were presented by John Barnard (“Computer manipulation of large virtual combinatorial libraries for diversity analysis and subset selection”), Bill Fisanick (“Datamining the CAS databases for biological activity”), Val Gillet (“Reduced graphs as descriptors of bioactivity”), Nick Jones (“Quantum mechanical modelling in the cheminformatics age”) and Markus Wagener (“Potential drugs and non-drugs: prediction and identification of important structural features”).

The Internet formed the basis not only for one of the sessions, but also for the Keynote Address (by Steve Heller on “The Internet and electronic publishing”), and for several of the product reviews and posters. Perhaps the Web’s principal characteristic is its unrivalled ability to act as a communication and integration tool, providing an effective, and exceedingly efficient, way of linking both people and computer systems. Its use as a human communication tool was discussed by Engelbert Zass (“Experiences with Web-based tools in teaching chemical information”) and by Bill Town (“The ChemWeb Chemistry Whiteboard – an aid to communication of chemical information in a virtual community”), while the latter application formed the basis of the presentations by Ray Carhart (“Adding chemical objects and operators to SQL: experiences with ORACLE 8i Data Cartridge technology”), Wolf-Dietrich Ihlenfeldt (“Dataflow programming in a WWW environment”) and Andrew Payne (“Cross-domain integration in the life sciences – the role of CORBA and the Object Management Group”) .

The Web session also included three papers on the handling of chemical reaction data. Hartmut Braun (“The Chemical Workbench – a reaction-centred synthesis design tool) described a system that has been developed at Hoffmann La Roche to enable bench chemists to design classical medicinal chemistry, small-scale parallel and full combinatorial syntheses; Heinz Matuszczyk discussed the clustering of hitlists resulting from searches of reaction databases (“Topology-based reaction classification – an important tool for the effective management of reaction information”); and Marco Durante (“The prediction of organic reaction products: determining the best reaction conditions”) considered methods for predicting which solvents will best stabilise a reaction transition state.

The final session covered a range of topics, although the analysis and representation of conformational flexibility formed the basis for most of these papers. Novel methods for modelling flexible molecules were described by Christof Schwab (“Addressing conformational flexibility”) and Miklos Vargyas (“A novel treatment of conformational flexibility using interval analysis”), while there were also two papers on flexible docking, by Carol Baxter (“A new approach to molecular docking and its application in screening compound databases”) and Uta Lessel (“Reference panel optimisation for Flexsim-X: a method to detect molecules with similar biological activity”). Docking methods are appropriate only where structural information is available for the biological target of interest; when this is not the case, molecular similarity methods provide a valuable alternative, as discussed by Gerry Maggiora (“Field-based similarity forcing: a conformationally flexible approach to molecular matching”). The last paper was by Eugene Babaev (“Example of successful prediction of biological activities”), who described the use of the PASS substructural analysis program to predict the activities of several novel classes of heterocycles, and the conference closed with a panel discussion that summarised the main points of the conference .

I am sure that those who attended the conference found, as I did, that it lived up to the high reputation of its predecessors; for those who did not attend, some of the paper presentations, and the concluding panel discussion, formed the basis for live “webcasts” as Event 17 in VEI’s ChemWeb Virtual Lecture series (see chemweb.vei.co.uk). In addition, it is expected that many of the papers mentioned above (as well as some of the poster presentations) will appear in published form in a forthcoming special issue of the Journal of Chemical Information and Computer Sciences. In conclusion, I would like to take this opportunity to thank the Chemical Structure Association Trust for the award of a bursary to support the attendance of my research group at the conference, the sixth of which is provisionally planned for June 2002.

Peter Willett, University of Sheffield

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Photo of attendees at Noordwijkerhout

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Sponsorship and Bursaries for the Noordwijkerhout meetingThe Chemical Structures conference was attended by over 170 scientists from academia and industry, representing 19 countries. The conference organisers wish to thank everyone who took part in the conference, but in particular would like to thank the 15 organisations which contributed to the sponsorship or to the bursary fund. Their generosity had a significant effect on the success of the meeting. The following companies sponsored events at the conference:

  • Chemical Abstracts Service
  • Molecular Design Ltd
  • Hampden Data Services
  • Cambridge Crystallographic Data Centre
  • Oxford Molecular
  • ACD

In addition, ChemWeb sponsored the conference web site (chemweb.com/conference/5ICCS/5ICCS.htm) and ISI sponsored the conference folders

23 academics from Russia, Poland, Thailand, Switzerland, Italy, Belgium, Germany and the UK were able to benefit from the bursary fund of about £6000, contributed by:

  • Chemical Structure Association Trust
  • CINF
  • KNCV (Dutch Chemical Society)
  • NSCS (New Swiss Chemical Society)
  • GlaxoWellcome
  • FIZ Chemie
  • Pfizer

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Photo of recipients of bursariesBursaries

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Beilstein CrossFire EcoPharm: Bringing a Valuable New Resource to the Research Scientist The success of Crossfire within the University and Industrial sectors has, along with other Information technology resources such as SciFinder from CAS, caused a revolution in the searching of chemical information. The key to the success is the enabling of the end user – principally, but not exclusively, the research chemist, to access reported data without fear of running up costly bills via a client/server interface that is intuitive and easy to use.

With the development of high-throughput discovery and the generation of more chemical and biological data than ever before, scientists often lack the information they need to decide which compounds to advance—and, more importantly, which ones to discard at a early stage. Toxic in vivo and environmental effects, instability, and poor biomobility are just some of the costly factors that can halt progress on promising leads.

CrossFire EcoPharm, a major new initiative from Beilstein, brings together pharmacological, toxicological, and ecotoxicological data from 180 leading journals, 60 of which are new journals indexed specifically for reports in these fields. The database is the only electronic collection indexing the original scientific literature for data in all three of these areas, making it a valuable resource for a broad cross-section of academic and industrial scientists.

The new datastructure, which will be an add-on to Crossfire and therefore fully integrated will be available in late summer of 1999. The indexing, design and management of such a massive new collection has taken many man years of effort on the part of the team in Frankfurt.

The University sector will be an early adopter and all Universities in the CHEST consortium for Scandinavia will automatically gain access to the new datastructure. In the UK higher Education, there will be a trial period to gauge the desirability and usage of the new indexing, and if all proves positive those Universities wishing to participate will be “switched on” to the new database.

Stephen Briggs sbriggs@beilstein.com UK Account representative

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FORTHCOMING CONFERENCESChemistry and the Internet, ChemInt’99, Georgetown, Washington D.C. Full details of this conference are given at chemint.org.

The Program is given below.

Friday 24th Sept

  • Noon – 6:00 pm Registration
  • 1:00 pm Synopsys Workshop
  • 3:00 pm ACD Labs Workshop
  • 6:00 pm Sponsor and Exhibitor Presentations
  • 7:00 pm – 8:00 pm Reception

Saturday 25th Sept

  • 8:00 am – Noon Registration
  • 8:00 am Breakfast
  • 9:30 am – 4:30 pm Exhibits Open
  • 9:00 am – 9:15 am Opening Remarks
    Steven Bachrach, Northern Illinois University

    Session 1: Economic Issues/E-Commerce

  • 9:15 am Clemens Jochum, Deutsche Bank
    Electronic Commerce: Can you trust a virtual Business Partner?
  • 10:00 am Coffee
  • 10:30 am Jerome Reichman, Vanderbilt University, School of Law
    Database Protection at the Crossroads: Recent Developments and the Long Term Perspective
  • 11:15 am – Noon – Panel Discussion on E-Commerce
    Panel Chairman: Wendy Warr, Wendy Warr & Associates
    Panel Members: Louis Culot, CambridgeSoft; Clemens Jochum, Deutsche Bank; Jeff Leane, Chemdex; Bill Town, ChemWeb; Patrick van der Valk, Chem Connect
  • Noon – 12:45 pm — Lunch Sponsored by Elsevier Science
  • Poster Session 12:45 pm – 2:00 pm

    Session 2: E-Publishing
    Chairperson: Stephen R. Heller

  • 2:15 pm Chris Parkinson, Battelle Pacific Northwest National Laboratory
    Collaborative Authoring with the EMSL Remote Document System
  • 2:35 pm Robert Bovenschulte, ACS
    10 Big Questions about Electronic Journals: Muddling Our Way Through Controversies and Uncertainties
  • 3:15 pm Coffee
  • 3:45 pm Steven M. Bachrach, Northern Illinois University
    The Internet Journal of Chemistry – A Status Report
  • 4:30 pm Panel Discussion on e-publishing
    Panel Chairman: Stephen R. Heller
    Panel Members: Mark Doyle, APS (doyle@aps.org); Lorrin Garson, ACS (lgarson@acs.org); Randy Marcinko, High Wire Press (randy@marcinko.com); Henry Rzepa, Imperial College (h.rzepa.ic.ac.uk)
  • 5:45 pm – Dinner on your own

Sunday 26th Sept

  • 7:30 am Breakfast

    Session 3: Education 8:45 am – Noon
    Chairperson: TBA

  • 8:45 am Steven S. Zumdahl, University of Illinois at Urbana-Champaign
    Teaching Introductory Chemistry Using the Internet
  • 9:15 am Alan Arnold, University College (UNSW)
    Gateways to Chemical Information – the MetaChem and Janus Projects Down-Under
  • 9:30 am – 4:30 pm – Exhibits Open
  • 10:00 am – Coffee
  • 10:30 am Karl Harrison, Oxford University
    Incorporating Multimedia into Chemistry Courseware. Examples from Oxford University
  • 11:15 am Robert Lancashire, University of the West Indies
    Interactive Web Page Development with CHIME and JAVA
  • 11:35 am Lon J.I>Concept and Realization of Bayer’s Integrated Chemistry Information System on the Corporate Intranet
  • 4:30 pm Panel Discussion on Corporate Internet/Intranets
    Panel Members: Joe Cerro, Bayer USA (joseph.cerro.b@bayer.com); Phil Kutzenco, Cytec (kutzenco@cytec.com); Yvonne Martin, Abbott Labs (yvonne.c.martin@abbott.com); Thomas Pierce, Rohm & Haas (thpierce@rohmhaas.com);
  • Dinner on your own

Monday 27th Sept

  • 8:00 am Breakfast

    Session 5: Databases

  • 8:45 am Stephen Boyer, IBM Almaden Research Center,
    The IBM Intellectual Property Network – An Internet Resource to Search, View, Retrieve Copies of Patents (and Patent Applications) from Around the World
  • 9:30 am Gary Mallard, NIST
    The NIST Chemistry WebBook
  • 10:15 am – Coffee
  • 10:45 am Lewis Jardine, Cherwell Scientific
    ChemSymphony Beans for Chemistry Clients and Database Access
  • 11:05 am Marc C. Nicklaus, NIH/NCI
    Enhanced CACTVS Browser of the Open NCI Database: Second Round
  • 11:35 am Closing Remarks, Henry Rzepa, Imperial College, London

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11th International Chemical Information Conference, Annecy The International Chemical Information Conference and Exhibition series began in Montreux in 1989. The 1999 conference will be held in the attractive city of Annecy in France, just over the border from Geneva in Switzerland. The exhibition will be held simultaneously with the conference in the conference venue, the Impérial Palace in Annecy. The program is given below. For full details, see http://www.infonortics.com/chemical/index.html

The cost of the conference is £595 and booking can be made online with a secure order form (see http://www.infonortics.com/chemical/99admin.html).

Monday 25 October 1999

Welcome cocktail and buffet dinner sponsored by Chemical Abstracts Service

Tuesday 26 October 1999

Session One: The changing technology environment for scientific and technical information

  • Patricia Rougeau, MDL Information Systems, California, USA
    The impact of new technology on chemical information management
  • David Evans, Claritech Corporation, Pennsylvania, USA
    Text mining for information co-ordination and discovery
  • René Deplanque and V. Schubert, FIZ Chemie, Berlin, Germany
    A network for chemistry education
  • James Myers, Environmental Molecular Sciences Laboratory, Washington, USA
    eResearch: The rise of scientific virtual facilities

Session Two: The changing business environment for scientific and technical information

  • Robert Massie, Chemical Abstracts Service, Ohio, USA
    SciTech information at the millennial boundary
  • John Regazzi, Elsevier Engineering Information, New Jersey, USA
    Re-inventing the database business. Getting from the 1990s to the 2000s
  • Martin White, TFPL, London, England
    Changes in the legal and regulatory environment for information: what users need to know
  • Pierre Buffet , Questel-Orbit, Paris, France
    Does value added information any longer have a strategic value?
  • Georg Schultheiss, FIZ Karlsruhe, Germany
    Classic online hosts in the scientific and technical information area: the need for new strategies for the new millennium
  • New product presentations by CAS, ISI, Springer-Verlag, Oxford Molecular, Bizint Solutions

Wednesday 27 October 1999

Session Three: Developments in the area of patent information

  • Liliane Meyers, European Patent Office, Munich, Germany
    Delivering patent information [provisional title]
  • Victoria Veach, 3M Information Services, Minnesota, USA
    Changes in patent searching brought about by the availability of web-based resources
  • Peter Rusch, California, USA
    Transitions for value-added patent information services
  • Michael Hehenberger, IBM Global Business Intelligence Solutions, NY, USA
    Text Mining of chemical and patent literature
  • Peter Kallas, BASF, Ludwigshafen, Germany
    CD-ROM archives: will the internet consign them to history?

Session Four: Data and sources for chemical and patent information

  • Ulrich Kämper, Wind GmbH, Cologne, Germany
    Chemical business information, competition from the internet
  • Huyen Nguyen, Beilstein Informationssyteme, Frankfurt, Germany
    A full-scale data compilation of pharmacology, toxicology and ecological chemistry into a single bibliographical source: CrossFire EcoPharm
  • Valeri Kulkov, Advanced Chemistry Development, Ontario, Canada
    A corporate solution for structure-based chromatography and spectroscopy management
  • Wolf-Dietrich Ihlenfeldt, University of Erlangen-Nürnberg, Germany
    The NCI database: bringing the largest open structure database to the www
  • David Lide, CRC Handbook, Maryland, USA
    Chemical property data sources in the internet era
  • New product presentations by INPI, DATEC, Chemical Concepts, STN International

Thursday 28 October 1999

Session Five: The changing concepts in scientific and technical information

  • Stephen E Arnold, AIT, Kentucky, USA
    The software revolution: a state of the art survey
  • Jane Whittall, SmithKline Beecham Pharmaceuticals R&D, Harlow, England
    Leveraging knowledge across continents
  • Daniel Champlon, C Corlay, E Nocera, Institut Français du Pétrole, Rueil-Malmaison, France
    Knowledge management implementation in an R&D centre
  • Stefano Caporusso, Dow Europe, Horgen, Switzerland
    Is the internet influencing business and technical information?
  • Irmgard Fischli, Novartis Pharma, Basel, Switzerland
    Re-creating corporate information departments following mergers and changes: some lessons and opportunities for the new century
  • End of 1999 programme at approximately 13.00

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3rd International Conference for Chemical Information Users, Manchester The third in this successful series of conferences will be held in Manchester, UK, on 16-17 November 1999. The first and second conferences were held in 1993 and 1995 respectively, and after a gap of four years there have been a number of developments in the chemical information world.

The conference will have three main themes:

  1. Electronic Journals and Document Delivery, a topic of interest to all information professionals. The speakers in this session will include Harry Boyle, CAS; Elspeth Hyams, Director of the Institute of Information Scientists; and Diana Leitch, John Rylands Library, University of Manchester.
  2. Education and Industry: Information Training for Chemists. This session will examine the information skills which are considered to be of value by the chemical and pharmaceutical industry, and review ways in which our universities are equipping graduates with these skills. We are delighted to welcome back Englebert Zass from ETH, Zürich, who has also spoken at the previous two conferences in the series to great acclaim. Other speakers in this session will be Wendy Warr, Wendy Warr Associates; Mark Winter, University of Sheffield; Barry Dunne, Science Information Systems.
  3. New Methods of Representing Chemical Structures on the Web. This will provide a timely overview of the subject. There will be a variety of speakers from academia, industry and information providers, including Peter Murray-Rust, University of Nottingham; Bill Town, ChemWeb; John Hollerton, Glaxo-Wellcome, and representatives from MDL and Synopsis. They will review products available, talk about on-going research in the area and try to predict the future in this important and rapidly developing field.

There will also be an exhibition where suppliers will provide information and demonstrations of their products. A conference dinner, sponsored by ChemWeb and e a pre-dinner reception sponsored by Beilstein Information Systems, will provide plenty of opportunity for discussions with the speakers, exhibitors and colleagues.

The venue is the Manchester Conference Centre at UMIST, just a few minutes walk away from Piccadilly railway station which has direct links to Manchester Airport, London and other UK destinations.

<p”>The conference is being organised jointly by the CSA and RSC-CIG, assisted by members of the Manchester team involved with organising the previous conferences in the series. We are pleased to be able to offer discounts to CSA and RSC-CIG members, as well as to academics. There will be a daily rate available, which will make the event appealing for those unable to come for the two days or who may only be interested in part of the programme. Further information is available at ChemWeb’s website, at chemweb.com/conference/manchester.html. To attend the conference, please download the registration form and return it to Dot Snow.

Helen Schofield (helen.schofield@umist.ac.uk)

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PRODUCT NEWSChemWeb.com ChemWeb.com, the Worldwide Club for the Chemical Community, has reached 100,000 members. The 100,000th member is Professor Herbert M. Geller, of the Department of Pharmacology at Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, US. Professor Geller received a Palm III Connected Organiser from ChemWeb.com at a presentation in Philadelphia on June 22nd. ChemWeb.com membership has increased by over 400% over the past year making it one of the largest groups of chemists in the world.

ChemWeb, Inc. has launched a new free Alerting Service. The first components of this new service to go live are the ChemWeb.com Article and Database Alerts. Members can register for this service free of charge, selecting journals or databases they wish to monitor for new updates. They will then receive an email alert each time new content is added to any of these selected journals or databases. This opt-in service allows chemists to keep in touch with updates to the specific journals and databases of relevance in their day-to-day work. The Alerting Service will be expanded to other areas of the Club in the future.

The ChemWeb.com Alerting Service can be signed up for at:

chemweb.com/article-alerts; and

chemweb.com/db-alerts;

768 books from New York-based publisher Marcel Dekker, Inc. have been added to the ChemWeb.com Shopping Mall. Dekker titles include key works in chemistry, engineering, biology, medicine, mathematics and statistics, environmental science, food science, and agriculture. With the addition of Marcel Dekker’s books, the ChemWeb.com Shopping Mall now carries over 2157 books from 12 different publishers, including Butterworth Heinemann, John Wiley & Sons, Oxford University Press and Kluwer Academic Publishers. It also offers some 232 software items from 23 suppliers, including CambridgeSoft Corporation, and labware from 5 manufacturers, including Mettler-Toledo Ltd. and Nicolet Instruments.

ChemWeb, Inc. has recently announced a new collaboration between ChemWeb.com, and

SciQuest.com, the efficient solution for sourcing, buying and managing scientific products used by the clinical, pharmaceutical, biotechnology, university and industrial markets. SciQuest.com will make their products available to ChemWeb.com’s members through a new storefront in the ChemWeb.com Shopping Mall.

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Advanced Chemistry Development IncACD Inc has now given away over 21,000 copies of their structure drawing package, Chemsketch (for full details please see http://www.acdlabs.com/). They have worldwide agreements with a number of pharmaceutical companies, including Pfizer, GlaxoWellcome and Astra and are in collaboration with a number of other companies (see http://www.acdlabs.com/news.html)

A lot of interest was expressed at HPLC ’99 in the two new products ChromManager, a chromatography data management system, and HPLC simulator, which allows you to input one or more chemical structures and then predict the relative retention times on a high performance liquid chromatography column.

ACD has integrated its state-of-the-art physical property, systematic naming and spectral prediction tools with alternative structure drawing packages. The prediction and naming tools are available using the ChemDraw package as the structure drawing interface.

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CambridgeSoftChemOffice Ultra 2000 is one of the world’s premier desktop chemistry software and includes ChemDraw Ultra, Chem3D Ultra, and ChemFinder Ultra, a seamlessly integrated suite that fulfills the day to day needs of chemists. You can draw reaction mechanisms for publication and visualize 3D molecular surfaces, orbitals and molecular properties. New features include Beilstein’s AutoNom, Connolly surfaces, and ChemFinder for Microsoft Excel 97. ChemDraw and Chem3D browser plugins are provided to enable access via the web. For more information on the contents of ChemDraw Ultra, Chem3D Ultra and ChemFinder Ultra, and other new products from CambridgeSoft please visit http://www.camsoft.com/.

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Oxford MolecularOxford Molecular has updated and enhanced DIVA, its desktop decision support application for life sciences research.

DIVA is an excellent tool for working with chemical information because it allows chemical structures and associated data to be stored, displayed and manipulated together in an integrated spreadsheet-like environment. It is designed to handle large datasets such as combinatorial libraries and high-throughput screening results.  It contains powerful, easy-to-use visualization and analysis techniques such as:

  • interactive histograms and 2D/3D graphs
  • graphical correlation analysis
  • recursive partitioning (FIRM)

You can now download a free demo version of DIVA from

www.oxmol.com/getinfo/cisd

The demo has several pre-prepared examples, including an illustration of how recursive partitioning can be used to analyze results of HTS on a combinatorial library.

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CASJust released this summer, STN on the Web means web-browser access to the complete content and functionality of STN. This is not a simplified access tool but rather a full-powered resource for information professionals and advanced “end-users”. STN on the Web is designed to work with Netscape Navigator 4.x and Microsoft Internet Explorer 4.x, with JavaScript enabled.

This service connects you with the more than 200 databases in the STN International network, including the CHEMICAL ABSTRACTS (CA) and Registry files. The complete set of STN commands is available along with graphic chemical structure searching and such convenient browser features as CAS Registry Number hyperlinks, images integrated with text, and context-sensitive help. Full-text documents for literature and patents, and STN user documentation, are just a click away. For a sense of how much substance information CAS has to offer, learn about the 20 millionth registered substance at http://www.cas.org/20million.htm.

STN on the Web offers a structure drawing editor (as in the popular STN Express personal computer sofware) that you can acquire as a free plug-in. Just look for the Structure Assistant button on the toolbars.

You can access STN on the Web at:

stnweb.cas.org/ (for North America)

stnweb.fiz-karlsruhe.de/ (for Europe)

European customers who need to set up an STN account may access the necessary form at the following URL: www.fiz-karlsruhe.de/stn/contract/conditio.html

For more information send a message to help@cas.org

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MDL Information Systems IncSample Management and Reagent Tracking (SMART) from MDL Information Systems, Inc., is a modular software application designed for enterprise-wide management of material inventories in high-throughput discovery environments. SMART provides a core set of modules that address and integrate the workflow of managing inventory throughout its life cycle from pre-acquisition through container disposal. The Web-based interface simplifies access to a material’s location, availability, restrictions, costs, hazards, and MSDS safety data. It includes business functions such as shopping for commercial reagents, ordering and tracking in-house reagents, bar coding samples at the receiving dock, and searching by chemical structure, name, or manufacturer.

MDL acquired Interactive Simulations, creator of award-winning 3D structure visualization software. The acquisition follows upon an earlier partnership in which the companies integrated Interactive Simulations’ SCULPT, a system for retrieving and displaying animated chemical structures from compound databases. SCULPT’s 3D graphics execute molecular simulations in real time, over 100 times faster than other commercially available products.

Distributed by MDL to cheminformatics groups under an exclusive license with Spotfire, Inc., the Spotfire suite includes modules that let scientists perform sophisticated, visual data analysis; link Spotfire analyses to other scientific data sources, such as chemical structure databases; and create and distribute reports on corporate intranets. The Spotfire product suite offers modular tools visually interrogating large data sets and communicating analysis results throughout the enterprise. For more information on MDL Information Systems, Inc. and products, visit http://www.mdli.com/

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PersonaliaCongratulations are due to Eleanor and David Ricketts on the birth of their little boy Corin, who arrived on 24 May 1999. Having moved to Cambridge Combinatorial to become Operation Manager, Eleanor is currently on maternity leave.

Congratulations too to Keith and Cathy Davies on the birth of Sarah on 13 June. Cathy is now on maternity leave from Oxford Molecular Group’s Chem-X development team.

Congratulations to Elizabeth and Vincent van Geerestein on the birth of their second daughter, Joy Iheoma, born on 28 March 1999.

Sandra Ward has joined TFPL as Executive Director and Head of a new Information Management Group.

Julian Hayward and Keith Harrington have been promoted: they are now Directors of Synopsys Scientific Systems.

Andrew Lyall has been appointed Chief Information Officer at Oxford GlycoSciences.

Edward Hodgkin is now at Tripos in St. Louis, as senior director, contract and discovery research for the Americas and Asia.

After 15 years with MDL Information Systems, Alex Kos is embarking on a new career, although he will continue marketing MDL products in Eastern Europe and Israel. Alex has founded a company in Switzerland, A. Kos Consulting & Solutions. He is also involved in another company Material Science International Services, GmbH (http://www.msiwp.com/) which provides data, software products, tools and services which support the development of new materials. A colleague of Alex’s, Dusan Toman of Dimension5 (http://www.dimension5.sk/), has developed a software package called DataMiner to visualise all sorts of data. He will continue to market MDL products in the Slovak Republic.

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