Wit

http://www.cme.msu.edu/WIT

WIT helps users reconstruct metabolism from complete bacterial genomic sequences.

Chemical Compounds

ChemFinder

http://chemfinder.camsoft.com/

ChemFinder is a database containing thousands of chemical compounds, including, for each compound, physical property data, chemical structures, and links to external information.

National Toxicology Program http://ntp-server.niehs.nih.gov/

The NTP website contains information about the Program, Chemical Health & Safety Data, 2D and 3D chemical structures, and abstracts of Short-Term Toxicity and Long-Term Carcinogenesis studies.

Enzymes and Genes

Ligand Chemical Database for Enzyme Reactions http://www.genome.ad.jp /dbget /ligand.html

LIGAND contains entries for enzymes and their substrates, products, and cofactors. GenBank

http://www.ncbi.nlm.nih.gov/Web/Genbank/index.html

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.

Microorganisms

World Data Center for Microorganisms http://wdcm.nig.ac.jp/

The WDCM provides a comprehensive directory of culture collections, databases on microbes and cell lines, and a getaway to biodiversity, molecular biology, and genome projects.

Bacterial Nomenclature Up-to-Date

http://www.gbf-braunschweig.de/DSMZ/bactnom/bactname.htm

This site, compiled by the DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkuturen GmbH, includes all bacterial names that have been validly published since January 1, 1980, and nomenclatural changes which have been validly published since then.

Source: From Ref. 34.

scribes using a knowledge of existing biodegradative enzymes to design new pathways to metabolize polyhalo-genated compounds (10). The UM-BBD could clearly stimulate similar projects by compiling and disseminating the crucial information needed to design such pathways de novo. We briefly describe the present status of the UM-BBD, including its format, use and users, peer acceptance, scientific advisory board, and future plans.

Format

In its first year of operation, the UM-BBD has evolved a standard format for reaction and compound pages. Both can link to many other internal and external information sources. One reaction page, for the first step in the biodegradation pathway for 1,2-dichloroethane, and a few of its many links, are shown in Figure 1. The Entrez Medline link (Fig. 1e) is especially interesting. The link back to the UM-BBD is prominent at the top. Also, when Entrez added a protein structure database, at our request they inserted the "Structure" link that is seen at the top of Figure 1e, so that our users would be only a click or two away from viewing and manipulating any available tertiary structure of the enzymes contained in the UM-BBD. Such a display for haloalkane dehalogenase is shown in Figure 1b. The

Figure 1. Selected windows of information from the UM-BBD, as viewed on a computer screen, representing the range of information available using the first reaction of 1,2-dichloroethane ca-tabolism as an example. The respective windows are organized with the reaction page at the center and links from a to e at the periphery, starting with a in the upper-left corner and going counterclockwise. The six windows are (centei) the haloalkane dehalogenase reaction page, (a) a reaction GIF showing the substrate and product structures, (b) a RasMol depiction of the haloalkane dehalogenase structure, (c) the enzyme page from the Kyoto Ligand Chemical Database, (d) the Entrez/Medline report on a selected paper on haloalkane dehalogenase, and (e) the 1,2-dichloroe-thane compound page.

Figure 1. Selected windows of information from the UM-BBD, as viewed on a computer screen, representing the range of information available using the first reaction of 1,2-dichloroethane ca-tabolism as an example. The respective windows are organized with the reaction page at the center and links from a to e at the periphery, starting with a in the upper-left corner and going counterclockwise. The six windows are (centei) the haloalkane dehalogenase reaction page, (a) a reaction GIF showing the substrate and product structures, (b) a RasMol depiction of the haloalkane dehalogenase structure, (c) the enzyme page from the Kyoto Ligand Chemical Database, (d) the Entrez/Medline report on a selected paper on haloalkane dehalogenase, and (e) the 1,2-dichloroe-thane compound page.

UM-BBD now includes links to graphics of enzyme reaction mechanisms on selected reaction pages. An index to graphics helps users find them (11). The usefulness of a database is a function both of the information it contains and the access users have to this information.

Initially, the only way to access UM-BBD information was through browsing lists of pathways, reactions, and compounds. As the UM-BBD grew, browsing became an increasingly less convenient mode of access. The ability to search the database was then added (12). At present one can search for compounds by full or partial name or synonym (e.g., toluene or methyl benzene), CAS registry number (e.g., 108-88-3), or formula (e.g., C7H8), and for enzymes by full or partial name (e.g., urease) or full or partial EC number (e.g., 3.5.1.5 or 3.5.1). This search option will continue to be developed with input from the UM-BBD user community and may be expanded in the future to include chemical substructure searches.

Use and Users

Two months after the UM-BBD initially appeared on the Web, we began collecting use statistics. Usage has grown continuously; use statistics by Internet domain for 1997 are shown in Table 2. Currently, the UM-BBD has approximately 80,000 accesses per month (Fig. 2). U.S. educational (30%) and industrial (20%) users together make up half of all present use (Table 2). UM-BBD users are invited to "sign our guestbook" (i.e., voluntarily complete a seven-item electronic form). Those who sign are given the option

Table 2. UM-BBD Use Statistics by Domain from January 1 to December 31, 1997

#reqs

%bytes

Domain

Brew Your Own Beer

Brew Your Own Beer

Discover How To Become Your Own Brew Master, With Brew Your Own Beer. It takes more than a recipe to make a great beer. Just using the right ingredients doesn't mean your beer will taste like it was meant to. Most of the time it’s the way a beer is made and served that makes it either an exceptional beer or one that gets dumped into the nearest flower pot.

Get My Free Ebook


Post a comment