Biomedical subjects

Thomas Wetter

Publications and source records attributed to Thomas Wetter.

3 recordsLinked to original sources

PubMed2003

Functional classification of proteins using a nearest neighbour algorithm.

With the large volume of genomic data being analysed nowadays it becomes extremely important to provide automated ways of protein classification to give the scientist a good overview of the analysed data. The system described here is very flexible and can be used with any given protein classification scheme. Before using the system, it has to be trained with a set of already classified proteins. Afterwards, other proteins can be classified by the system automatically. Several tests have been performed to assess the quality of this classification; they have shown the usefulness of the system. The system will be available as part of a commercial software package.

Algorithms↗

PubMed2002

Increase in amino acids in the pons after sleep deprivation: a pilot study using proton magnetic resonance spectroscopy.

Total sleep deprivation (TSD) is an efficient method to relieve depression. An involvement of GABAergic and glutamatergic neurotransmission in the pathophysiology of depression and the mechanism of action of TSD has been suggested. To directly assess the content of GABA, glutamate (Glu) and glutamine (Gln) before and after TSD, we estimated their concentrations in four brain regions in six healthy subjects using proton magnetic resonance spectroscopy. The unresolved estimate of GABA, Glu and Gln, as well as GABA and Gln were increased in the pons after 24 h of TSD, the effect being prominent in three subjects. There were no significant changes in the hypothalamus, thalamus or parietooccipital cortex. These preliminary data support earlier animal data and indirect findings in humans suggesting that GABA and Gln, especially in the pontine structures, may play a key role in the mechanism of TSD.

Adult↗

PubMed2002

Rapid generation of a representative ensemble of N-glycan conformations.

Glycosylated proteins are ubiquitous components of extracellular matrices and cellular surfaces where their oligosaccharide moieties are implicated in a wide range of cell-cell and cell-matrix recognition events. Glycans constitute highly flexible molecules. Only a small number of glycan X-ray structures is available for which sufficient electron density for an entire oligosaccharide chain has been observed. An unambiguous structure determination based on NMR-derived geometric constraints alone is often not possible. Time consuming computational approaches such as Monte Carlo calculations and molecular dynamics simulations have been widely used to explore the conformational space accessible to complex carbohydrates. The generation of a comprehensive data base for N-glycan fragments based on long time molecular dynamics simulations is presented. The fragments are chosen in such a way that the effects of branched N-glycan structures are taken into account. The prediction database constitutes the basis of a procedure to generate a complete set of all possible conformations for a given N-glycan. The constructed conformations are ranked according to their energy content. The resulting conformations are in reasonable agreement with experimental data. A web interface has been established (http://www.dkfz.de/spec/glydict/), which enables to input any N-glycan of interest and to receive an ensemble of generated conformations within a few minutes.

Carbohydrate Conformation↗