Issue 51

Newsletter

Issue 51

March 1999

Features

The Cambridge Crystallographic Data Centre (CCDC)The Cambridge Crystallographic Data Centre (CCDC) is the international repository for the crystal structures of small organic and organometallic compounds. These are stored in the Cambridge Structural Database (CSD), copies of which are distributed, together with its accompanying search software, to over 600 academic institutions in 50 countries, and to more than 100 commercial sites worldwide. The Data Centre was founded in 1965 by Dr Olga Kennard FRS, as part of the Chemistry Department at the University of Cambridge, UK. The CCDC became an independent not-for-profit institution in 1989, retaining close links to the University. In 1997, Dr Kennard retired as Director, and has been succeeded by Dr David Hartley as Executive Director and Dr Frank Allen as Scientific Director.

The Cambridge Structural Database remains at the very core of CCDC activities, and is expanding at an accelerating rate due to improvements in the technologies and techniques of crystallography. There is an ever greater flood of data to be handled, and the CCDC is adapting to cope with this, in order to keep the CSD complete, accurate and up-to-date. CSD search software is being re-engineered to make it more accessible, including support for Windows NT, and a new, much more flexible and user-friendly graphical interface is being developed. In keeping with its academic origins and history, the CCDC continues to maintain a lively research presence, through in-house projects and a number of very active external collaborations that address new applications of the accumulated data.

However, to promote the application of its rapidly increasing archive of crystallographic information amongst a wider audience, the CCDC is now developing a range of new products and services derived from the CSD. The CCDC has already released IsoStar, a library of intermolecular interactions, which is distributed alongside the CSD itself. IsoStar is a knowledge-based product, in that it encapsulates information that is inherent in the complete 200,000-structure database on how particular organic functional groups like to interact with other groups. This derived knowledge is presented to the user in the form of graphical scatterplots or contour plots. The more than 15,000 plots effectively provide interaction probabilities for chemical entities which are readily accessible via a Web browser interface. An intramolecular sister product, a library of torsional distributions and other molecular geometry, is currently under development.

This derived knowledge can then be put to good use in problem solving, and the CCDC is beginning to make the presence of crystallographic data felt here too. The GOLD program, available from CCDC, and jointly developed with the University of Sheffield and GlaxoWellcome, is a protein-ligand docking program that makes use of intermolecular interaction information and conformational knowledge extracted from the CSD. GOLD has firmly established itself as a leading product in its application area. Coming soon is SuperStar. This is a purely knowledge based application which builds directly upon IsoStar by combining interaction probability maps for functional groups to produce interaction-probability surfaces for protein active sites, further aiding computational studies of protein – ligand binding. Several other avenues for application of crystallographic knowledge are currently being explored by the CCDC itself, or in collaboration with academic and commercial organisations worldwide.

The CCDC has entered a period of onward development. Its original science-driven ethos and activities remain and, indeed, are being strengthened. The overall aim of the Centre, though, has always been to promote the application of crystallographic information for the benefit of science. Thus, the development of new products is an additional focus through which the CCDC is pursuing its aims and objectives with renewed vigour.

Dr. Stephen J. Maginn,
Support and Marketing Manager,
Cambridge Crystallographic Data Centre (CCDC)

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Puzzling Over Chemical NamesWorking chemists would much prefer to be left to their own devices to come up with names for the compounds they discover. Names that trip off the tongue, names that twist it. Names that honour colleagues, the famous, hometowns and occasionally slime moulds, are all much nicer than sticking to the rules. So what’s in a name? as the man said, and why shouldn’t we keep it trivial?

The Chemical Abstracts Service has a chemical counter on its web site that tells visitors there are 19 million (19,205,313 at the time of writing), which averages a staggering 400,000+ molecules added each year since CAS started. Each compound is assigned a unique CAS registry number, a simple task, presumably.

The numerical identifier, the registry code, allows scientists trawling the literature, and the Internet, to pinpoint an exact chemical structure. CAS, bless it, also does the really dirty job of providing a unique systematic name for each of those compounds. From this name a reasonably competent chemist should be able to work out the formula and so build their own molecular model.

Things are never quite so simple though and while CAS uses one set of rules, IUPAC opts for a different method. As every chemistry undergraduate, hard done to CAS employee, and technical editor on a chemical journal knows, however, naming a new compound is no simple task. Occasionally likened to puzzling over the Times Crossword, chemical nomenclature is almost a deeply satisfying vocation for those carrying a raw chemical structure through to systematic name. Or, it’s a waste of notepad and pencil, depending on your stance.

What’s the answer? Chemists have known for years: trivial names provide the clue. Why bother rifling through page after page of IUPAC’s blue, red and green books and CAS directories and rule books when you can simply come up with something suitable off the top of your head and have done with it. The earliest alchemists didn’t seem to worry too much about cyclic molecules with names to set you spinning, such as {4,34-dimethyl- 1,4,7,10,13,16,19,22,25,28,31,34,37,40,43,46,49,52,55, 58- icosaazatricyclo[56.2.2.2.2.2.7,10,28,31,37,40]hexacon tane} when they had phlogiston and philosopher’s wool (sic) to play with. When it comes to trivia chemists can let their imaginations run wild.

No one would imagine you could be arrested for snorting 3-benzoylmethyl-2-tropanecarboxylic acid through a short piece of tubing, but if you refer to this clinical-sounding white powder by its trivial name of cocaine, you would be a little more wary about what enters your olfactory passages. Numerous pharmaceuticals and drugs of abuse can cause a major headache when it comes to providing them with a standardised name. Take two tablets of ortho-acetylsalicylic acid and see if you feel better in the morning.

Some of the 19 million lend themselves to trivialisation because of what they do or their shape. Multidentate chelating agents such as the crown ethers have a bit of an ethereal character and are shaped like coronettes. Other members of this group of chemical hosts have been given names to reflect how well they can trap their guests. The names of cryptands, sepulchrands and cavitands all have a deathly ring to them although their “proper” names would not sound quite so fearsome despite taking you to the graveyard shift just to work them out. While German chemists have just come up with a molybdenum compound that resembles a Keplerean planetary system. So do they go for the full systematic name? No, they call it keplerate.

One bright chemical star to receive its name, rank and serial number in the CAS registry is the buckminsterfullerene molecule. Named for the architect, Richard Buckminster Fuller, who designed the huge geodesic structures for Expo ’67 in Montreal, the C60 molecule has amazingly a rather succinct systematic name: [60]fullerene, which on this occasion is actually shorter than its trivial name.

Fig1: Buckyball: where would you start in creating a systematic name for a ball?

 

 

Some chaotic molecules known trivially as the starburst dendrimers come a little way down to earth as cascade polymers. These three-dimensional divergent molecules branch from a core and are finding themselves the centre of much attention as potential mimics of biomolecules, such as proteins. Trying to use a systematic name for something with generation after generation of branching polymer strands though might leave you tied up for a day or two to say the least.

Trivial monikers often have more purpose than glorifying architects or reminiscing about tombs. Classes of enzymes are generally names following simple rules to help the biochemists and molecular biologists. The name might even hint at what a particular enzyme does. For instance, horse liver alcohol dehydrogenase one might correctly deduce is from the lobal abdominal glandular organ of a land-mammal (genus Equus) and converts hydroxys into ketones. Simple, hey?

 

Fig2: Crown ether: going round in circles

In a similar vein, the steroidal hormones that course through our bodies at various stages of our lives would not so much course as trickle with their full systematic names. Much more fluid are the likes of pregnenone and testosterone. Again, their names even hint at what particular life processes and organ activity they might be involved in.

It is easy to make fun of systematic nomenclature (easier than doing it, anyway) but without it very little chemistry would actually get done. Imagine having to think of a unique, succinct and sexy name for every one of the 19 million plus substances around along the lines of buckyball, keplerate, carbon tet., or whatever. Trivia has its place, of course, especially in emergencies when looking up the name on the bottle in CAS before neutralising the spilt acid is not really an option. And, acetone will always be acetone no matter how many laboratory technicians you try to convert.

However, there is no substitute for a systematic way to identify particular compounds uniquely and allow any chemist to know exactly what structure is being discussed. After all, there’s usually a chemical editor somewhere who quite likes doing crosswords.

 

Fig3 Viagra: would it have been such a rising star with its systematic name?

 

David Bradley is a freelance science writer and former technical editor for some of those chemistry journals. He can be contacted through his web site at Sciencebase Science News. A version of this article appeared in The Alchemist on http://www.chemweb.com/

David Bradley
Sciencebase Science News

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AGM and New Executive Committee

AGM Round Up

The 1998 AGM was held at the Linnean Society on 7th December 1998. Full Minutes are given under “Committee” on this web site, or are available from the Secretary, Barbara Nicholson.

Virtual Executive Committee Meetings

There were four Executive Committee meetings during 1998, one of which had been a “Virtual Live” meeting held, by courtesy of ChemWeb, through VEI. This was an interesting experiment, but because only a few people were able to receive the live audio, and others had technical problems with firewalls, it had limited success. On the other hand, the electronic Executive Committee meetings held using e-mails via the Executive Committee listserver, over a period of a week, are extremely successful, and many action items are completed during the course of a meeting.

Co-operation with other organisations

The most progress during the year was in the area of co-operation with other organisations: the joint MGMS/CSA meeting held last April in Sheffield was excellent and resulted in a profit for the CSA of over £1800. £2000 was donated from the CSA to the CSA Trust in 1998. The CSA was also a technical sponsor for the ChemInt98 meeting in Irvine, California. Again this was a very successful meeting, although there were no applications for the student bursaries that were offered.

A joint RSC-CIG/CSA meeting was held in London in October on Patents and Competitor Intelligence, which included very interesting papers – some of the papers are up in the Meetings section of this web site.

In 1999, the co-operation with other organisations continues with the following joint or co-sponsored meetings:

  • The 5th International Conference on Chemical Structures from 6th-10th June which is to be co-sponsored by the CSA
  • A joint CSA/CINF session at the ACS Fall meeting in New Orleans, on “Online versus the web”
  • A second Chemistry and the Internet meeting, ChemInt’99, at Georgetown University, Washington D.C. Sept 25-27 1999
  • The third International Conference for Chemical Information Users at Manchester in November, jointly sponsored with the RSC-CIG.

Membership, Newsletter and website

3 Newsletters were produced in 1998 and the web site was kept reasonably well up-to-date, with password protection added, allowing members only to access the latest Newsletter. Current paid-up membership stands at just over 150, but several members have not yet paid for 1998! There are now CSA members in UK, US, Germany, Switzerland, France, Netherlands, Belgium, Denmark, Italy, Russia, India and Japan. The Committee will concentrate on publicity, particularly overseas, in 1999.

The New Executive Committee

The Committee would like to thank the retiring members of the Exec. – Barrie Walker and John Holliday – for all the work they did for the Executive Committee during their time in office.

Change of President

A vote of thanks was given to Mike Lynch who wished to stand down as President.

The Committee welcomed Peter Willett as our new President

Targets for 1999

  • Keep momentum going
  • Publish 3 newsletters
  • Ensure the web site is current
  • Work on publicity – particularly overseas
  • Pursue joint meetings

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Constitution Amendment

Constitution amended to allow Executive Committee Members to serve longer!

At the AGM, it was agreed that Article 5.2.3 would be amended to allow Executive Committee members to serve for a longer period.

Article 5.2.3 of the constitution previously stated that:

“Officers are elected for a period of two years, ordinary members are elected for one year only. Officers and ordinary members of the Executive Committee may submit themselves for re-election, but may serve for no more than 4 consecutive years at a time, except that an Officer may serve for a fifth consecutive year in order to complete a two year term”.

It was unanimously approved at the AGM that the length of service be extended to 6 years and that Article 5.2.3 should be amended to read:

5.2.3 “….Officers and ordinary members of the Executive Committee may submit themselves for re-election, but may serve no more than 6 consecutive years at a time, except that an Officer may serve for a seventh consecutive year in order to complete a two year term”

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New Executive Committee Member

Helen Schofield

Upon graduating in chemistry at Manchester University I worked for Derwent Publications and then the International Union of Crystallography. After completing a post-graduate diploma in librarianship, I was appointed the chemistry subject specialist at UMIST Library. I run the chemistry department library and am also now an honorary lecturer in the Chemistry Department, involved with teaching chemical information skills. I have research interests in the history of the chemical literature, patent information usage, and was involved in the DTI-funded Valid Analytical Measurement sampling programme. I also carry out all patent searching at UMIST. I now work for part of my time for MIDAS (at Manchester Computing), which supplies the Beilstein CrossFire database to the UK academic community; my role is to provide training courses throughout the UK and Scandinavia.

Helen Schofield (Chemistry Dept, Library and MIDAS CrossFire Service)
UMIST
PO Box 88
Sackville St
Manchester
UK, M60 1QD
Tel.: 44-161-200 4420
Fax: 44-161-200 4941
Email: helen.schofield@umist.ac.uk

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New President

Peter Willett

Peter Willett obtained an Honours degree in Chemistry from Exeter College, Oxford in 1975 and then went to the Department of Information Studies, University of Sheffield where he obtained an MSc in Information Studies. Following doctoral and postdoctoral research on computer techniques for the processing of databases of chemical reactions, he joined the staff of the University as a Lecturer in Information Science in 1979 and was awarded a Personal Chair in 1991.

He is a Fellow of the Institute of Information Scientists, and was the recipient of the 1993 Skolnik Award of the American Chemical Society for his contributions to chemical information science and of the 1997 Distinguished Lecturer Award of the New Jersey Chapter of the American Society for Information Science for his contributions to information science. He is a member of the editorial boards of Information Retrieval, Journal of Combinatorial Chemistry, Journal of Documentation, Journal of the American Society for Information Science, Journal of Chemical Information and Computer Sciences, and SAR and QSAR in Environmental Research, and has been involved in the organisation of many national and international conferences in various aspects of information retrieval.

Professor Willett heads a large research group studying novel computational techniques for the storage and retrieval of information in textual, chemical and biochemical databases and has over 320 publications describing this work. His current interests include the development of conflation methods for text searching, database applications of genetic algorithms and automatic classification methods, computational techniques for the analysis of molecular diversity, and the processing of 3-D chemical structure data to support research in drug discovery and protein engineering.

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Next AGM and Dinner

Date for your diary:

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 and the Dinner will be at 7.00 for 7.30 pm, by popular request back at the Cadogan Hotel, Sloane Street.

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Meeting announcements

3rd International Conference for Chemical Information Users, ManchesterPreliminary announcement and call for papers

The third conference in this successful series will be held on 16-17 November 1999, at the Manchester Conference Centre, UMIST, UK.

The themes of the conference will be:

  • Electronic Journals and Document delivery
  • Education and Industry – Information Training for Chemists
  • Chemical Structures on the Web

If you are interested in presenting a paper at the conference, please send a title, abstract and your contact details to Dot Snow, at Dot.Snow@agrevo.com

If you wish to exhibit at the meeting, please contact Don Parkin at d.parkin@dl.ac.uk

The following invited speakers will be addressing the key issues of interest to Chemical Information Users as the Millennium approaches: Engelbert Zass, ETH Zurich Diana Leitch, University of Manchester Mark Winter, University of Sheffield Bill Town, ChemWeb Peter Murray-Rust, University of Nottingham

The conference will be sponsored by the Royal Society of Chemistry Chemical Information Group and the Chemical Structure Association. The organising committee are: Janet Ash, Diana Leitch, Peter Nichols, Don Parkin, Peter Regan, Helen Schofield, Dot Snow, Doug Veal, Andy Whiting, Peter Willett

For further information and to register for the conference, please visit the web site at http://chemweb.com/conference/manchester.html

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Fifth International Conference on Chemical StructuresSunday, June 6 through Thursday, June 10, 1999 Leeuwenhorst Congress Center, Noordwijkerhout, The NetherlandsSponsors:

  • Chemical Structure Association (CSA)
  • Chemistry-Information Division of the Society of German Chemists (GDCh)
  • Division of Chemical Information of the American Chemical Society (ACS)
  • New Swiss Chemical Society (NSCS)
  • Royal Netherlands Chemical Society (KNCV)
  • Royal Society of Chemistry, Chemical Information Group (RSC)

The following organisations have also generously agreed to sponsor the conference: ACD, Cambridge Crystallographic Data Centre, Chemical Structure Association Trust, FIZ Chemie Berlin, Hampden Data Services, ISI, MDL, Oxford Molecular, Pfizer.

The International Conference on Chemical Structures brings together an international group interested in handling chemical structures and related topics. Participants discuss research and development in the processing, storage, retrieval and use of chemical structures. The conference fosters cooperation among organizations and researchers involved with chemical structures and chemical information.

The International Conference on Chemical Structures brings together an international group interested in handling chemical structures and related topics. The conference will be held at the Leeuwenhorst Congress Center, Noordwijkerhout, the Netherlands, which is a modern comprehensive centre, with recreational facilities, only 2 km from the dunes and easily reached from Schipol airport and by train from major European cities.

Technical Program

The conference will start with a keynote address on Sunday afternoon followed by a traditional Rijsttafel dinner. A list of papers that will be presented in the plenary sessions is given below and additional papers might be selected by the Scientific Review Committee. Over fifty posters will round out the scientific program.

Session A – Combinatorial Chemistry: Library Design

  • Wendy A. Warr, Wendy Warr & Associates, Trends in Combinatorial Chemistry.
  • Eric Martin, Chiron Corp., Sensitivity Analysis and other Improved Tools for Combinatorial Library Design and Mixture Representation.
  • Dimitris K. Agrafiotis, 3-Dimensional Pharmaceuticals, Inc., Advances in the Design and Visualization of Combinatorial Libraries.
  • Peter Johnson, University of Leeds, De Novo Design of Synthetically Accessible Ligands.
  • Robert D. Brown, Molecular Simulations, Inc., Structure Based Design of Combinatorial Libraries.
  • Gianpaolo Bravi, GlaxoWellcome UK, Optimisation of 3D Libraries with PLUMS.
  • Peter Grootenhuis, CombiChem, The Design of Maximum Information Libraries as a Highly Efficient Tool for Lead Generation and Evolution.

Session B – Combinatorial Chemistry: Diversity, QSAR

  • John M. Barnard, BCI Ltd, Computer Manipulation of Large Virtual Combinatorial Libraries for Diversity Analysis and Subset Selection.
  • Stephen D. Pickett, Rhone-Poulenc Rorer, Enhancing Hit-To-Lead Properties of Diverse Libraries.
  • Trevor Heritage, Tripos Inc., High Throughput and Combinatorial qSAR.
  • Valerie J. Gillett, University of Sheffield, Reduced Graphs as Descriptors of Bioactivity.
  • Markus Wagener, NV Organon, Potential Drugs and Non-Drugs: Prediction and Identification of Important Structural Features.
  • Nick Jones, Oxford Molecular Group, Quantum Mechanical Modeling in the Cheminformatics Age.
  • William Fisanick, Chemical Abstracts Service, Datamining the CAS databases for Biological Activity.

Session C – Web Applications, Reactions, ChemInformatics

  • Wolf D. Infeldt, University of Erlangen-Nuremberg, Dataflow Programming in a WWW Environment.
  • Andrew Payne, NetGenics UK Ltd., Cross Domain Integration in the Life Sciences – The Role of CORBA and the Object Management Group.
  • Bryan Vickery, ChemWeb Inc., The ChemWeb Chemistry Whiteboard – An Aid to Communication of Chemical Information in a Virtual Community.
  • Engelbert Zass, ETH Zuerich, Experiences with Web-Based Tools in Teaching Chemical Information.
  • Hartmut Braun, Hoffmann La Roche, The Chemical Workbench-A Reaction-Centered Synthesis Design Tool.
  • Heinz Matuszczyk, InfoChem GmbH, Topology-Based Reaction Classification: An Important Tool for Efficient Management of Reaction Information.
  • Marco Durante, Universita’ degli Sudi di Milano, The Predicting of Organic Reaction Products: Determining the Best Reaction Conditions.
  • Raymond E. Carhart, MDL Information Systems, Inc., Adding Chemical Objects and Operators to SQL: Experiences with Oracle(TM) 8i Data Cartridge Technology.

Session D – Modeling, Similarity, QSAR

  • Christof H. Schwab, University Erlangen-Nòrnberg, Addressing Conformational Flexibility.
  • Miklos Vargyas, University of Leeds, A Novel Treatment of Conformational Flexibility Using Interval Analysis.
  • Baxter, Proteus Molecular Design Ltd., A New Approach to Molecular Docking and Its Application in Screening Compound Databases.
  • Gerald M. Maggiora, Pharmacia & Upjohn, Field-Based Similarity Forcing: A Conformationally-Flexible Approach to Molecular Matching.
  • Uta Lessel, Boeringer Ingelheim Pharma KG, Reference Panel Optimization for Flexsim-X – A Method to Detect Molecules With Similar Biological Activity.
  • Eugene V. Babaev, Moscow State University, Example of Successful Prediction of Biological Activities.
  • Dmitrii Filimonov, Institute of Biomedical Chemistry RAMS, Multilevel Neighborhoods of Atoms as the Sub-Structure Topological Descriptors for Predicting the Bioactivities and Properties of Compounds.

Registration and Fees

Registration for the entire conference, including full board and four nights lodging, excursion and conference dinner, and conference proceedings is Dfl 1650 for single room accommodation (Dfl 1500 per person for double room accommodation). There is a student discount of Dfl 125. To register, download the registration form from the conference web site http://chemweb.com/conference/5ICCs/5ICCS.htmland fax the form to Dr. Vincent van Geerestein +31 412 662 539. (Voice: +31 412 661 882).

Exhibition

If you wish to exhibit at the conference, please contact Dr. Rainer Moll . A limited number of exhibition spaces have been set aside free of charge for academic participants to demonstrate and discuss their projects. All exhibitors must register for the conference.

Further information can be found on the conference web site at http://chemweb.com/conference/5ICCs/5ICCS.htmlor contact the Chairman of the Organising Committee, Dr. Guenter Grethe.
Dr. Guenter Grethe
MDL Information Systems, Inc.
14600 Catalina Street
San Leandro, CA 94577
USA
+1 510 895-1313 (ext.1430) [voice]
+1 510 614-3638 [fax]
guenter@mdli.com

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CSA Trust

Donations to the Trust

The Trustees of the Chemical Structure Association Trust are very grateful to Chemical Abstracts Service and to Elsevier for two very generous donations of $5000 each to the Trust funds this year.

The Trust has also received generous contributions from FIZ Chemie Berlin, GlaxoWellcome and Pfizer totalling £2200 to be used for bursaries for the Fifth International Conference on Chemical Structures at Noordwijkerhout in June. There have been 24 applications for bursaries for the conference and details of the successful applicants will be given in the next CSA Newsletter.

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CSA Trust Bursaries

Bursaries Available from the CSA Trust

In addition to bursaries specifically for the Chemical Structures conference in Noordwijkerhout, the Chemical Structure Association Trust is offering £1000 for bursaries to assist with conference fees and/or travel for ANY conference in 1999 which is related to the aims of the Trust. The Trust is an internationally recognised registered Charity which promotes education, research and development in the field of storage, processing and retrieval of information about chemical structures, reactions and compounds. Eligible conferences include, but are not limited to:

Bursaries will be awarded on merit. Preference will be given to people who wish to submit a paper or poster at a conference and who are unable to meet their own conference expenses.

To apply for a bursary, please send the following to Janet Ash by 1st July 1999:

  1. A brief biography
  2. Details of your current research work
  3. Details of which conference you wish to attend, giving the relevance to your current work.
  4. The title of any paper or poster that you wish to present.
  5. A letter of recommendation from a supervisor or colleague.

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Awards

CSA Trust Award

CSA Trust 1999 Award

Applications are invited for the 1999 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:

  1. A statement of academic qualifications
  2. Details of relevant work and a statement of research recently completed by the applicant
  3. The purpose for which the award is required. The clarity and relevance of this statement will be crucial in the evaluation of the applicants
  4. 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 of 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 31st July 1999, preferably by e-mail, to the Chairman of the Awards sub-committee, Professor Michael Lynch
Any postal applications should be sent to:
Janet Ash
Secretary of the Chemical Structure Association Trust
The Roundel
Frittenden
Cranbrook
Kent, TN17 2EP
UK

The Award will be presented at the International Chemical Information Meeting in Annecy in October.

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Tony Kent Strix AwardNominations for the 1999 Award are now invited, and should be sent with full supporting documentation to:

Alan Gilchrist,
Editor, Journal of Information Science,
32 Friar Road,
Brighton BN1 6NH,
U.K.

The closing date for nominations is Friday 18th June 1999.

The Strix Award is in memory of Dr Tony Kent, a past fellow of the U.K. Institute of Information Scientists, who died in 1997. Tony made a major contribution to the development of information science and information services in the U.K. and internationally, particularly in the field of chemistry.

The Award is given to an information worker in recognition of an outstanding practical innovation or achievement in the field of information retrieval. This could take the form of an application or service, or overall past achievements from which significant advances have emanated. The Award is open to individuals or groups from anywhere in the world. Nominations will be judged by a panel of experts, including the recipient of the 1998 Award, and the statuette of an owl will be presented to the winner after the Institute’s AGM in September. The name Strix was chosen to reflect both Tony’s interest in ornithology, and the name of one of the last and most successful information retrieval packages which he created.

A small booklet, containing some contributions from colleagues is available from the Institute Office (price £4.50, profits to the Strix Award Fund): 44 – 45 Museum Street, London WC1A 1LY

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Ernie Hyde Award

Peter Nichols wins the CSA Ernie Hyde award

Congratulations to Peter Nichols on winning the 1998 Ernie Hyde award. There can be few people who have contributed so much to the CSA over such a long period of time. Peter was one of the original CNA(UK) members, and he has served for two 4-year periods as Chairman and is now Vice-Chairman.

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Company and Product News

Tripos News

Tripos and Scripps Bioinformatics Research CollaborationYields New GeneFoldTM Gene Screening Software

Tripos, Inc. (NASDAQ: TRPS) announced the release of GeneFoldTM, a protein fold identification software tool, developed in collaboration with Professors Jeffrey Skolnick and Adam Godzik of The Scripps Research Institute (La Jolla, CA). GeneFold is the first success product launched in an ongoing two-year agreement between the two organizations to develop bioinformatics software applications for drug discovery. The agreement began in spring 1998.

GeneFold bridges the gap between Tripos’ unique expertise in the area of cheminformatics and the expanding need for gene sequencing, allowing the wealth of knowledge in bioinformatics to be applied to drug design. Specifically, GeneFold helps researchers by identifying protein folds, or structures, that a given sequence is most likely to fit. By combining sequence-based alignment with structural information, it results in a method that is far more sensitive and selective to fold recognition than either method alone. When combined with Tripos’ ComposerTM to build a 3D model, GeneFold provides a truly unique tool for protein structure modeling.

GeneFold provides greater accuracy with an improved scoring function and has been validated on six genomes including E.coli and yeast.

The Scripps Research Institute, based in La Jolla, California, is one of America’s largest private biomedical institutes. It is internationally recognized for its basic research into molecular and cellular biology, chemistry, immunology and neurosciences.

Tripos, Inc. is a discovery research organization with unique expertise in molecular informatics. Tripos supplies software, research services, and compound libraries to the pharmaceutical, biotechnology and other life science industries worldwide. The customer base includes the world’s largest scientific research organizations as well as the rapidly growing biotechnology companies.

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Cambridge Soft CorporationChemDraw Pro, the world’s most popular chemical drawing package, works with all major enterprise and desktop chemical databases. Search by structure and substructure, using automatic reaction mapping and specifying atom and bond properties for precise results. Publish in print using style templates and on the Web with the ChemDraw Plugin. Display spectra, structure, and annotations on the same page – in print or on the Internet. Use ChemDraw’s structure cleanup and chemical intelligence to draw accurate, chemically correct structures and reaction diagrams.

ChemDraw Ultra adds ChemNMR, ChemProp, and Name=Struct to ChemDraw Pro. Analyze structures by estimating physical properties and NMR shifts (1H and 13C) with simple menu selections. Create structures from chemical names and common names.

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ACD Product News

Name 3.6

ACD are offering Name Pro (which uses the IUPAC naming conventions) and Index Name Pro (which uses the CAS naming conventions) software for the special price of $1995 for a stand-alone copy of either package($995 academic). For details, see http://www.acdlabs.com/products/name/iupac.html or http://www.acdlabs.com/products/name/cas.html respectively

ChemFolder integrated with Name Pro 3.6

Owners of Name Pro and ChemFolder can generate the IUPAC name from *within* ChemFolder. ChemFolder is a general-purpose chemical databasing software that stores structures, values, file pointers, etc. For more details, please refer to:

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CAS Online back to 1907While giants of twentieth century science from Marie Curie to Glenn Seaborg were publishing their early work,CHEMICAL ABSTRACTS (CA) was recording it for future research. Today,Chemical Abstracts Service (CAS) online databases reach back to 1967; to find the earlier works, researchers need to consult print or microfilm. But CAS is now making chemistry-related literature and patents from 1907 to 1967 accessible online, creating a digital compendium of the entire century’s scientific discoveries. CAS, the world’s premier chemistry-related information resource, made the announcement today during the 217th American Chemical Society (ACS) national meeting in Anaheim, California.

CAS has captured CA abstract titles, author names, and patent assignees in electronic form. They can all be searched by names and keywords in the CAOLD file on STN International. “CAS is opening up an additional sixty years of scientific literature online for easy search and retrieval,” said CAS Director Robert Massie. “That amounts to more than 3 million documents from 1907-1967, including nearly 800,000 patents.”

“Scientific research of all kinds began to accelerate in the first half of this century,” observed CA Editor David Weisgerber. “Among many other areas of investigation recorded in CA volumes before 1967 were studies of natural products for medicinal purposes, which is a topic of renewed interest to today’s chemists and pharmaceutical laboratories.”

CA abstracts prior to 1967 have been available for display in the CAOLD file in image format since 1998, but the online indexing that enables researchers to identify abstracts of interest has been very limited for pre-1967 material. For example, it has been possible to identify substances discussed in the older documents by searching CAS Registry Numbers, but only back to the mid-1950’s.

In addition to making information since 1907 available for online searching on STN, CAS will release the CA 10th and 11th Collective Indexes on CD-ROM. 10CI covers the period from 1977 through 1981, and 11CI covers 1982 through 1986. Their search interaction will be the same as that of CA and the 12CI and 13CI on CD-ROM. A total of 23 years of Chemical Abstracts will now be available on CD-ROM.

For pricing and other details about CAS products, contact CAS Customer Service at
1-800-753-4227 (toll-free within North America) or 614-447-3700.
Fax: 614-447-3751;
email: help@cas.org.

The CAS Web site is at http://www.cas.org/.

Eric Shively
CAS
eshively@cas.org

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MDL News

Cheshire for ISIS

Cheshire is a new software development environment for MDL’s ISIS that automates the process of analyzing, interpreting, and manipulating large volumes of chemical information by enabling chemistry application developers to write scripts for otherwise tedious tasks.

MDL Enhances Life Science Workbench to Streamline Protocol Definition and Data Collection

Life Science Workbench 1.1 New Components Get Biologists Back to the Bench MDL Information Systems, Inc. released version 1.1 of its biological data management system, the Life Science Workbench. The component-based system adds three new components, called “Managers,” that help biologists lay out complex experiments, interpret experimental results, and more quickly process the raw data generated by data acquisition devices: the Layout Manager, the Calculation Manager, and the Reader File Manager.

Streamling Reagent Selection/Procurement for High-Throughput Chemistry

MDL’s Reagent Selector is a configurable system designed to help synthetic, medicinal, and combinatorial chemists simplify and accelerate the complicated process of selecting and procuring reagents for medium- and high-throughput synthesis. In a single package, the system provides integrated tools for creating, filtering, clustering, sharing, and manipulating lists of reagents; locating and obtaining reagents from in-house inventories; and “shopping” for compounds from databases of commercial suppliers.

LitLink/Standard Server Provides One-Click Desktop Access to Literature Citations

LitLink/Standard Server is an electronic article broker enabling researchers to have one-click access to scientific literature cited in MDL Reaction Browser, in MDL Reaction Web, and in Beilstein Commander. When scientists select a citation, LitLink/Standard Server delivers the article to the desktop in a new Web browser window. LitLink/Standard Server is an out-of-the-box product, which is a subset of the fully customizable LitLink/Pro Server. LitLink/Pro Server has all of LitLink/Standard Server’s features plus the ability to customize almost any Windows or Web application to access virtually any Internet or intranet literature repository that has a query interface.

Reaction Web Extends Access of MDL’s Synthetic Methodology World-Class Databases into a Web-Based Intranet Application

In December, 1998, MDL Information Systems, Inc. announced at the Online Information 98 Conference in London, Reaction Web, a Web-based Intranet application that brings desktop access to synthetic methodology from MDL’s world-class synthetic methodology databases. When used with LitLink/Standard Server, Reaction Web links MDL’s synthetic methodology database search engine to several literature repositories. To retrieve an article, scientists select from references in MDL’s synthetic methodology databases, and Reaction Web locates the article and displays it onscreen. This enables the chemist to quickly verify a methodology selected from the database by examining experimental details in the original article.

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ChemWeb Young Chemistry Writer of the Year AwardChemWeb announces the launch of the International Young Chemistry Writer of the Year Award 1999. This year’s award is generously sponsored by Pharmacia & Upjohn http://www.pnu.com/ and the prize is $1,000 in cash and an expenses paid trip to the ACS Fall National Meeting in New Orleans in August 1999 where the winner will collect their prize. The winning article will also be published in The Alchemist.

The competition requires entrants to write a feature style article and is open to anyone aged 16-30. The closing date is the 30th June 1999. Full details and a copy of the rules are available at: http://chemweb.com/home/youngwriter.html

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New Members and PersonaliaPlease welcome several members from the USA who joined in the latter part of 1998:

Mrs Kay Kim, from the FDA
Ms Jennifer Liu, a Graduate Student Researcher at UCI.
Ms Mary-Anne Moore, CambridgeSoft Corporation
Dr John Rumble, NIST.

Also welcome to Dr. R. Lahana from SYNTEM in France and a welcome back to Chris White who is with the British Library. The newest member we welcome is Ms Shouko, who is working on chemical structure information systems with Fuji Photo Film in Japan.

Soichi Tokizane, who joined the CSA last year, has become the CSA representative in Japan. Mr Tokizane is now with JST.

Phil McHale has been promoted again and is now VP Product Marketing at MDL Information Systems

Eduard Cohen is the new Managing Director of Beilstein Information Systems. He joins Beilstein from another Elsevier company in Munich.

Bill Town, Director of Operations at ChemWeb, Inc. has been elected Chair-Elect of the American Chemical Society’s Chemical Information Division (CINF) for 1999, and will be CINF Chair for the year 2000. He will be the first non-US citizen to hold this post.

Peter Steele is now Managing Director of Current Patents Ltd. a company in the Current Science Group.

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