A database designed to serve as a comprehensive resource of data for botulinum research (Lebeda 2004), BotDB offers several features to aid in the research efforts of understanding the toxicity and finding ways to counteract the toxic effects of clostridial neurotoxins. There are seven distinct areas of navigation for BotDB: General Information, Literature, Neurotoxin, Protein Analysis, Sequence Analysis, Tools and Community.
Conferences lists a number of upcoming events for the community. Genomes (KEGG maps) lists Clostridium botulinum and Clostridium tetani genomes which have manually drawn pathway maps representing molecular interaction and reaction networks in KEGG databases.
In this section, users can query the botulinum and tetanus subset of citations. The queries are performed through botXminer, which is the first successful implementation of MEDLINE Extensible Markup Language (XML) articles in an object relational schema (Mudunuri et al. 2006). This method of storage offers the possibility of certain queries not feasible through PubMed. The 'Group Articles' section offers one such query and more will be added depending on user interest. Journals allows users to retrieve botulinum or tetanus related literature from several journals.
This section might be the one of interest to most botulinum researchers. Using the Sequence Graphical Query, users can retrieve the sequences of various molecules involved in any stage in the BoNT course of action on the nervous system. Similarly, Literature Graphical Query allows users to retrieve articles published. The 3D structures of all the BoNT and TeNT's can be viewed from the Structures section. Inhibitors section allows users to search candidate inhibitors using author name, IC50, inhibition site, inhibitor type, Ki, inhibitor name, PubMed ID, serotype, and structure. Kinetics section includes information on Kinetics Minimalist Model and is expected to expand with more models and simulations.
BotDB here provides a DSSP Analysis tool which summarizes secondary structure information by counting individual alpha helices, 3- and 5- helices, beta strands, beta bridges, hydrogen bonded turns, bends as well as other non-structural information extracted from a DSSP file.
Nucleotide and protein sequences can be annotated using the various sequences analysis tools: Blast, PSI-Blast, ClustalW, and SSearch. BotDB has extensive information on the nucleic and amino acid sequences of the clostridial neurotoxin genes and proteins. These are not available for querying in the current implementation but would be added to the sequence databases in the near future.
The IC50-to-Ki converter (Cer et al. 2009) computes Ki values from experimentally determined IC50 values for inhibitors of enzymes that obey classic Michaelis-Menten kinetics and of protein-ligand interactions.
BotDB welcomes input from the community and here you can submit new information you would like us to share with the rest of the community.
Notes on Graphical Viewers
Graphics viewer programs are provided to display botXminer search results, stored images and three-dimensional representations of protein structures.
Please send your questions, suggestions, or comments to botdb[AT]mail.nih.gov.
Last updated on July 28 2009