Biomedical subjects

Christian Ebeling

Publications and source records attributed to Christian Ebeling.

5 recordsLinked to original sources

PubMed2007

SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas.

To provide an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology the database SYSTOMONAS (SYSTems biology of pseudOMONAS) was established. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as gene-regulatory networks were stored. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration is realized using SOAP interfaces for the well established databases BRENDA, KEGG and PRODORIC. Several tools for the analysis of stored data and for the visualization of the corresponding results are provided, enabling a quick understanding of metabolic pathways, genomic arrangements or promoter structures of interest. The focus of SYSTOMONAS is on pseudomonads and in particular Pseudomonas aeruginosa, an opportunistic human pathogen. With this database we would like to encourage the Pseudomonas community to elucidate cellular processes of interest using an integrated systems biology strategy. The database is accessible at http://www.systomonas.de.

Bacterial Proteins↗

PubMed2007

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.

The BRENDA (BRaunschweig ENzyme DAtabase) enzyme information system (http://www.brenda.uni-koeln.de) is the largest publicly available enzyme information system worldwide. The major parts of its contents are manually extracted from primary literature. It is not restricted to specific groups of enzymes, but includes information on all identified enzymes irrespective of the enzyme's source. The range of data encompasses functional, structural, sequence, localisation, disease-related, isolation, stability information on enzyme and ligand-related data. Each single entry is linked to the enzyme source and to a literature reference. Recently the data repository was complemented by text-mining data in AMENDA (Automatic Mining of ENzyme DAta) and FRENDA (Full Reference ENzyme DAta). A genome browser, membrane protein prediction and full-text search capacities were added. The newly implemented web service provides instant access to the data for programmers via a SOAP (Simple Object Access Protocol) interface. The BRENDA data can be downloaded in the form of a text file from the beginning of 2007.

Animals↗

PubMed2004

BRENDA, the enzyme database: updates and major new developments.

BRENDA (BRaunschweig ENzyme DAtabase) represents a comprehensive collection of enzyme and metabolic information, based on primary literature. The database contains data from at least 83,000 different enzymes from 9800 different organisms, classified in approximately 4200 EC numbers. BRENDA includes biochemical and molecular information on classification and nomenclature, reaction and specificity, functional parameters, occurrence, enzyme structure, application, engineering, stability, disease, isolation and preparation, links and literature references. The data are extracted and evaluated from approximately 46,000 references, which are linked to PubMed as long as the reference is cited in PubMed. In the past year BRENDA has undergone major changes including a large increase in updating speed with >50% of all data updated in 2002 or in the first half of 2003, the development of a new EC-tree browser, a taxonomy-tree browser, a chemical substructure search engine for ligand structure, the development of controlled vocabulary, an ontology for some information fields and a thesaurus for ligand names. The database is accessible free of charge to the academic community at http://www.brenda. uni-koeln.de.

Animals↗

PubMed2004

Cytosolic processing of proteasomal cleavage products can enhance the presentation efficiency of MHC-1 epitopes.

The vertebrate immune system is able to detect abnormal body cells by the specific repertoire of 8 - 12 residues long peptides (= epitopes or peptide antigens) presented at the cell surface by the MHC-1 molecule complex. The generation of an epitope starts with the degradation of endogenous proteins into primary oligomeric fragments by cytosolic proteases, predominantly the proteasome. These primary fragments may be further attacked by various amino peptidases resident in the cytosol or, alternatively, may escape from this attack by entering the endoplasmic reticulum (ER) by the transporter associated with antigen presentation (TAP). To study the possible consequences of this scenario for the efficiency of antigen presentation we have applied kinetic modelling. The mathematical model comprises the generation of primary oligomeric fragments containing the definitive epitope, the successive N-terminal shortening of these primary fragments by cytosolic amino peptidases and the TAP-mediated transport of cytosolic peptides into the ER. Because the number of peptide molecules may become very small we have performed deterministic and stochastic simulations of the kinetic model. Our simulations show that cytosolic N-terminal trimming of primary fragments may drastically increase loading epitope precursors into the ER. In particular, a primary fragment generated with a low rate of TAP transport into the ER may nevertheless become a potent epitope precursor if at least one of its N-terminal trimming products will be efficiently transported.

Animals↗

PubMed2002

BRENDA: a resource for enzyme data and metabolic information.

BRENDA (BRaunschweig ENzyme DAtabase), founded in 1987 by Dietmar Schomburg, is a comprehensive protein function database, containing enzymatic and metabolic information extracted from the primary literature. Presently, the database holds data on more than 40 000 enzymes and 4460 different organisms, and includes information about enzyme-ligand relationships with numerous chemical compounds. The collection of molecular and biochemical information in BRENDA provides a fundamental resource for research in biotechnology, pharmacology, medicinal diagnostics, enzyme mechanics, and metabolism. BRENDA is accessible free of charge to the academic community at http://www.brenda.uni-koeln.de/; commercial users need a license available from http://www.science-factory.com/

Animals↗