Biomedical subjects

Frank J Lebeda

Publications and source records attributed to Frank J Lebeda.

3 recordsLinked to original sources

PubMed2006

botXminer: mining biomedical literature with a new web-based application.

This paper outlines botXminer, a publicly available application to search XML-formatted MEDLINE data in a complete, object-relational schema implemented in Oracle XML DB. An advantage offered by botXminer is that it can generate quantitative results with certain queries that are not feasible through the Entrez-PubMed interface. After retrieving citations associated with user-supplied search terms, MEDLINE fields (title, abstract, journal, MeSH and chemical) and terms (MeSH qualifiers and descriptors, keywords, author, gene symbol and chemical), these citations are grouped and displayed as tabulated or graphic results. This work represents an extension of previous research for integrating these citations with relational systems. botXminer has a user-friendly, intuitive interface that can be freely accessed at http://botdb.abcc.ncifcrf.gov.

Computer Graphics↗

PubMed2005

The structure of the neurotoxin-associated protein HA33/A from Clostridium botulinum suggests a reoccurring beta-trefoil fold in the progenitor toxin complex.

The hemagglutinating protein HA33 from Clostridium botulinum is associated with the large botulinum neurotoxin secreted complexes and is critical in toxin protection, internalization, and possibly activation. We report the crystal structure of serotype A HA33 (HA33/A) at 1.5 A resolution that contains a unique domain organization and a carbohydrate recognition site. In addition, sequence alignments of the other toxin complex components, including the neurotoxin BoNT/A, hemagglutinating protein HA17/A, and non-toxic non-hemagglutinating protein NTNHA/A, suggests that most of the toxin complex consists of a reoccurring beta-trefoil fold.

Amino Acid Sequence↗

PubMed2004

BotDB: A database resource for the clostridial neurotoxins.

BotDB is a database designed to encapsulate the rapidly expanding amount of information about the structure and function of the botulinum (BoNT) and tetanus neurotoxins and to track a variety of basic and applied research efforts. The AceDB management system was chosen for this project because of its flexibility in manipulating semistructured data sets and for its information retrieval query languages. In addition to storing amino and nucleic acid sequences of the clostridial neurotoxin genes and proteins, BotDB provides sequence data for new classes of objects, including neurotoxin mutants, substrates and their mutants, associated nontoxic proteins, and C-fragment vaccine candidates. New data types provide information on detection assays for the neurotoxins and on structural data from X-ray crystallographic and circular dichroism spectroscopic studies. Kinetic parameters from biochemical experiments include reaction rates for substrate cleavage and block of neurotransmission. The structures and kinetic characteristics of presently known chemical inhibitors are also being archived. All of these data are associated with citations of the relevant literature for on-line annotation. Graphics viewer programs are provided to display stored images and three-dimensional representations of protein structures. BotDB is in the alpha test phase of development and will become a publicly available Web site.

Amino Acid Sequence↗