Summaries

Summary of Information Sources

Click on the Icon to connect to the information source.
Click on the Question mark for full details.
Click on the Service Name for details of the provider of the service and if available a full tutorial and on-line help provided by them
The sections below summarise the objectives of each component. Your task is to analyse critically the results you get from each search.

Word/Claris and ChemDraw. The purpose of the lab is to show you how a project report on a selected topic can be prepared. By opening programs such as Microsoft Word or Claris Works and CambridgeSoft Chemdraw and cutting/pasting various graphic images between them, you can prepare a professional looking report "on-the-fly" as you acquire information. To copy any image present in a Netscape browser, point the mouse cursor over the image and hold the mouse button down until a menu appears. Select copy to "copy this image", then move to the Word/Claris window and paste the image using the item in the edit window. Text can be similarly captured. We also make use of an alternative program called Claris Home Page to compose Web pages. DO NOT attempt to start Claris Works on a Silicon Graphics workstation or a PC system: this program is not available on these systems in the department.

Enables a search of the local Chemistry Department Web pages.

The Bath Information Delivery System is an on line version of the science citation index, in which all primary papers published in essentially all the important chemical journals are indexed by subject, author, date and several other fields. By default, the search will start in the current year, e.g 2000, and currently goes back to 1981. You will be using the Web interface to search this database.

During the year 2000-2000, the BIDS ISI service will be transitioning from Bath to MIMAS (Manchester), where it will be known as Web-of-Science. Your ATHENS login should work here as well. Please fee free to try the new service out, and in your reports, comment critically on which of the two services provides a better search environment.

CAS On-line is the primary source of abstracted information on Chemistry. Some 18 million chemicals and 19 million records are contained on this database. There are three principal access mechanisms to CAS; a) a simple terminal based interface where commands are typed from the keyboard, b) a structure drawing interface called STN Express and c) a more complete information organising environment called SciFinder. Because CAS operates on a commercial basis, and the costs of using it can be very high, we will illustrate its use via method a), using small demonstration databases called LCA and LREG.

CD-ROM on-line is a collection of CD-ROM based databases available from the Central College library. The collection includes the Merck Index (under Biological Sciences), a very useful source of information on pharmaceutical substances.

Libertas: The College Libraries on-line catalogues. Interaction with either bulletin boards or information gleaned from say e-mail may lead to promising books or journals that you might wish to consult in the conventional printed form. You can quickly find out if this material is available in either the central College or departmental libraries by logging into the Libertas system. If it is, you can even reserve the material in your session. Please note that from December 2000, Libertas will be augmented and eventually replaced by a new system called Unicorn.

Hotbot is one of a series of "Indexing Robots" that trawl the Web indexing it. The default options presented can be augmented by "expert" mode. Alternatively, you can try a so-called Portal, which is in effect an aggregator for a number of different search engines. One called Copernic is available on our MacOS and Windows systems. Another implemented on MacOS is the Sherlock "find by content" search. Go to File/Find to invoke it. Try comparing the results obtained for a specific search by these various methods.

Daylight Information systems. Some chemical information companies make available on-line sub-sets of some of their databases. Daylight Information systems has pioneered innovative interfaces to such information. Here you can search the World Drug Index (WDI) for any information on your search topic. The results of this search are used to generate a so-called SMILES descriptor of any hits, which can in turn be used to search a current literature database called Savant. This can be used to generate synthetic methods for preparing compounds identical with, or similar to your search query. If you are really ambitious, try the "Grins" interface to structure building rather than using the SMILES string.

ChemFinder. Another large collection of molecular information is the ChemFinder Database database. This can be searched in a variety of ways, using different sorts of tools, including Browser plug-ins and Java-Interfaces. See what you can find for e.g. Penicillin.

The Beilstein Crossfire System. Here you will perform a search using the Beilstein database for specific property information about the compound. You should try to find out melting points of any compounds identified.

For tutorials and examples, see here.

Chemical Reaction Accessing using ISIS/Base Sometimes even information about a specific compound is too general to be useful. Much of chemistry is about the chemical transformation of one compound into another, whether it can be done at all or in good yield, what the reagents and conditions are etc. Such a search implies a quite subtle relationship between two or more compounds. Again, specialised software is needed for this task. You will be using a system called ISIS/Base. Here the end results of a search is not so much a file containing information about one compound, but one or more pages of information relating to the chemical transformation, including the literature citation. You will need to run two specific programs, staring with ISIS Base and then using ISIS Draw.

Chemical Concepts. This database illustrates searching for spectral properties based on (inter alia) chemical substructure searches. Various NMR nuclei are supported, including ¹H, ¹³C, ¹⁹F, and UV and Mass spectral information is also often available.

You will be using an X-Window program to run SpecInfo. Note that the Mac and the Windows computers use different X-Window programs. To invoke on a Mac, use the left hand Icon above, to invoke on Windows, use the second. A tutorial on how to create a structure search is given here. This tutorial assumes however that you are using a Unix workstation, and have access to a three-button mouse. The three buttons are referred to throughout the tutorial as LM (left mouse), MM (middle mouse) and RM (right mouse). On a Macintosh computer, you will be using an X-Window emulator that maps LM to the regular mouse button, and MM to the left cursor key of the numeric keypad on the keyboard. On Windows machines, MM is mapped to a SIMULTANEOUS press of the TWO mouse buttons (it can be quite difficult to press both at exactly the same time!). The use of MM in particular is crucial to a Specinfo structure search, since the structure is transferred from the editor to the search window using this button!

Try sketching Penicillin, and see if any spectral information for this or similar molecules exists, by following the steps given in the tutorial.

The Cambridge Chemical Database Centre. Whilst keywords based on the title of a paper or its authors may provide some useful information, this will not necessarily produce information about an individual chemical compound. Here the search must be defined by actually drawing the compound of interest, or even merely a "sub-structure" and then performing a systematic search based on this criterion rather than one based on text. This requires more specialised programs, and also as it happens a great deal more computer time. Here you will perform a sub-structure search on a database containing the 3D coordinates derived from crystal structure solutions. More complete documentation can be found here.

You will be using an X-Window program to run SpecInfo. Note that the Mac and the Windows computers use different X-Window programs. To invoke on a Mac, use the first Icon, to invoke on Windows, use the Second.

European Bioinformatics Institute This database contains all known protein and macromolecule crystal and NMR derived structures. A number of enzymes are known to act specifically on penicillins, either to digest them or to form them. You should use this database to find out whether any enzymes associated with the search query and what their 3D structures might be.

MedChem Explorer from MSI. This is a complete chemo-informatics environment for performing all manner of 3D modelling experiments on a molecule (or so-called combinatorial chemistry library). In this specific case, you will perform a 3D shape similarity experiment on your chosen project molecule, with the intention of seeking "3D similar molecules" in specified databases.

VChemLab and Molecules-of-the-Month are two current awareness local databases containing organised "stories" about specific molecules. Anyone writing an exemplary report could find themselves contributing to these databases!

Electronic Conferences. Start your search by visiting the ECTOC-3 and ECHET98 electronic conferences. These were the first electronic conferences with organic chemistry as a general theme.

Electronic Journals. Increasingly, journals are starting to appear in electronic and searchable form. Start your search by visiting Chemical Communications and JACS.

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