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27 papers found.
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Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training

Michael Meissner 0 Michael Schmuker 0 Gisbert Schneider 0 0 Address: Johann Wolfgang Goethe-Universitat, Institut fur Organische Chemie und Chemische Biologie , Siesmayerstrae 70, D-60323 Frankfurt

Architecture, function and prediction of long signal peptides

Jan A. Hiss Gisbert Schneider Protein targeting in eukaryotic cells is vital for cell survival and development. N-terminal signal peptides guide proteins to the membrane of the endoplasmic reticulum

Bacterial serine protease HtrA as a promising new target for antimicrobial therapy?

Recent studies have demonstrated that the bacterial chaperone and serine protease high temperature requirement A (HtrA) is closely associated with the establishment and progression of several infectious diseases. HtrA activity enhances bacterial survival under stress conditions, but also has direct effects on functions of the cell adhesion protein E-cadherin and extracellular ...

PocketPicker: analysis of ligand binding-sites with shape descriptors

Martin Weisel 0 Ewgenij Proschak 0 Gisbert Schneider 0 0 Address: Johann Wolfgang Goethe-Universitt , Beilstein Endowed Chair for Cheminformatics, Institut fr Organische Chemie und Chemische ... Martin Weisel. This project was based on the idea and realized under the guidance and consultation of Gisbert Schneider. Additional material Additional file 1 Four complexed and three unbound structures

Predicting olfactory receptor neuron responses from odorant structure

Background Olfactory receptors work at the interface between the chemical world of volatile molecules and the perception of scent in the brain. Their main purpose is to translate chemical space into information that can be processed by neural circuits. Assuming that these receptors have evolved to cope with this task, the analysis of their coding strategy promises to yield valuable ...

Go with the flow and accessorize your drugs

Gisbert Schneider 0 0 Department of Chemistry and Applied Biosciences, Eidgenossische Technische Hochschule (ETH) , Wolfgang-Pauli-Str. 10, 8093 Zurich , Switzerland The fast pace of drug discovery

Scrutinizing MHC-I Binding Peptides and Their Limits of Variation

Designed peptides that bind to major histocompatibility protein I (MHC-I) allomorphs bear the promise of representing epitopes that stimulate a desired immune response. A rigorous bioinformatical exploration of sequence patterns hidden in peptides that bind to the mouse MHC-I allomorph H-2Kb is presented. We exemplify and validate these motif findings by systematically dissecting ...

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds. The quality of the designed compounds is assessed by a graph kernel method measuring their similarity to known bioactive ...

Machine Learning Estimates of Natural Product Conformational Energies

Machine learning has been used for estimation of potential energy surfaces to speed up molecular dynamics simulations of small systems. We demonstrate that this approach is feasible for significantly larger, structurally complex molecules, taking the natural product Archazolid A, a potent inhibitor of vacuolar-type ATPase, from the myxobacterium Archangium gephyra as an example. ...

Sequential Anti-Cytomegalovirus Response Monitoring May Allow Prediction of Cytomegalovirus Reactivation after Allogeneic Stem Cell Transplantation

Background Reconstitution of cytomegalovirus-specific CD3+CD8+ T cells (CMV-CTLs) after allogeneic hematopoietic stem cell transplantation (HSCT) is necessary to bring cytomegalovirus (CMV) reactivation under control. However, the parameters determining protective CMV-CTL reconstitution remain unclear to date. Design and Methods In a prospective tri-center study, CMV-CTL ...

Prediction of Extracellular Proteases of the Human Pathogen Helicobacter pylori Reveals Proteolytic Activity of the Hp1018/19 Protein HtrA

Exported proteases of Helicobacter pylori (H. pylori) are potentially involved in pathogen-associated disorders leading to gastric inflammation and neoplasia. By comprehensive sequence screening of the H. pylori proteome for predicted secreted proteases, we retrieved several candidate genes. We detected caseinolytic activities of several such proteases, which are released ...

In Silico Adoption of an Orphan Nuclear Receptor NR4A1

A 4.1μs molecular dynamics simulation of the NR4A1 (hNur77) apo-protein has been undertaken and a previously undetected druggable pocket has become apparent that is located remotely from the ‘traditional’ nuclear receptor ligand-binding site. A NR4A1/bis-indole ligand complex at this novel site has been found to be stable over 1 μs of simulation and to result in an interesting ...

Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors

Background Molecular descriptors are essential for many applications in computational chemistry, such as ligand-based similarity searching. Spherical harmonics have previously been suggested as comprehensive descriptors of molecular structure and properties. We investigate a spherical harmonics descriptor for shape-based virtual screening. Methodology/Principal Findings We ...

Domain Organization of Long Signal Peptides of Single-Pass Integral Membrane Proteins Reveals Multiple Functional Capacity

Targeting signals direct proteins to their extra - or intracellular destination such as the plasma membrane or cellular organelles. Here we investigated the structure and function of exceptionally long signal peptides encompassing at least 40 amino acid residues. We discovered a two-domain organization (“NtraC model”) in many long signals from vertebrate precursor proteins. ...