Gerhard Barnickel

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LIGSITE is a new program for the automatic and time-efficient detection of pockets on the surface of proteins that may act as binding sites for small molecule ligands. Pockets are identified with a series of simple operations on a cubic grid. Using a set of receptor-ligand complexes we show that LIGSITE is able to identify the binding sites of small(More)
An atomic model of the conformation of peptidoglycan was taken as the basis for an analysis of packing patterns of the peptidoglycan strands in two- and three-dimensional arrangements. For the sake of clarity, glycan strands were approximated by cylindrical rods around which a continuous helix of possible peptide cross-linkage sites was arranged. Using the(More)
Preventing the formation of insoluble polyglutamine containing protein aggregates in neurons may represent an attractive therapeutic strategy to ameliorate Huntington's disease (HD). Therefore, the ability to screen for small molecules that suppress the self-assembly of huntingtin would have potential clinical and significant research applications. We have(More)
The conformational properties of the isolated S form of Salmonella sp. lipopolysaccharide (LPS), of Re mutant LPS, and of free lipid A were investigated by using X-ray diffraction and conformational energy calculations. The data obtained showed that LPS in a dried, in a hydrated, and probably also in an aqueous dispersion state is capable of forming(More)
Using the computer system PASS (prediction of activity spectra for substances), which predicts simultaneously several hundreds of biological activities, a training set for discriminating between drugs and nondrugs is created. For the training set, two subsets of databases of drugs and nondrugs (a subset of the World Drug Index, WDI, vs the Available(More)
Using the method of conformational energy calculations, favoured conformations of a pseudomurein sugar strand built up from beta 1,3-linked N-acetyl-D-glucosamine and N-acetyl-L-talosaminuronic acid were obtained. Such a completely beta 1,3-linked polysaccharide primary structure, although contrasting with the originally proposed alternating beta 1,3-alpha(More)
A three-step approach for multiscale modeling of protein conformational changes is presented that incorporates information about preferred directions of protein motions into a geometric simulation algorithm. The first two steps are based on a rigid cluster normal-mode analysis (RCNMA). Low-frequency normal modes are used in the third step (NMSim) to extend(More)
Conformational energy calculations have been carried out on N-acetyl-L-alanyl-D-gamma-glutamyl-L-lysyl-D-alanyl-D-alanine as a model of the peptide moiety of peptidoglycan. Although many conformations were of comparable energy, particular favoured conformations were selected by assuming conformational similarity between the pentapeptide and the tetrapeptide(More)
Infrared spectroscopic measurements are used to obtain insights into the three-dimensional architecture of peptidoglycan (murein), the rigid component of almost all bacterial cell walls. The infrared spectra of various types of peptidoglycans (including all chemotypes and examples of the so called A and B groups) were compared to each other and to those(More)