A Database Resource for Clostridial Neurotoxins

A database designed to serve as a comprehensive resource of data for botulinum (bot) 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 four distinct areas of navigation for BotDB: Literature, Neurotoxin, Sequence Analysis and Bot Community.

Literature:

In this section, users can query the bot 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.

Neurotoxin:

This section might be the one of interest to most bot 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 view inhibitors as well as search them using K_i or IC₅₀ values. Tables of synthetic and naturally occurring inhibitors of BoNT activity and binding, along with their inhibitory constants (including values for Ki, IC50s, time-to-50% block, etc.) are included with references in this section. Kinetics section currently holds information on Kinetics Minimalist Model and is expected to expand with more models and simulations.

Sequence Analysis

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.

Bot Community

Upcoming Conferences lists a number of upcoming events for the Bot 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 e-mail at botdb@ncifcrf.gov.

Sponsored by U. S. Army Medical Research Institute of Infectious Diseases (USAMRIID) in collaboration with the National Cancer Institute (NCI) and Advanced Biomedical Computing Center (ABCC).