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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...

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

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...

Prediction of Type III Secretion Signals in Genomes of Gram-Negative Bacteria

Background Pathogenic bacteria infecting both animals as well as plants use various mechanisms to transport virulence factors across their cell membranes and channel these proteins into the infected host cell. The type III secretion system represents such a mechanism. Proteins transported via this pathway (“effector proteins”) have to be distinguished from all other proteins that...

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...

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

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...

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...

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

Inhibitors of Helicobacter pylori Protease HtrA Found by ‘Virtual Ligand’ Screening Combat Bacterial Invasion of Epithelia

Gisbert Schneider 0 Paul Wrede, Charite-Universitatsmedizin Berlin, Germany 0 1 Institute of Organic Chemistry and Chemical Biology, Goethe-University , Frankfurt, Germany , 2 Division of Microbiology

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...

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

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...

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...

The Plasmodium Export Element Revisited

Gisbert Schneider 0 Per Westermark, Uppsala University, Sweden 0 1 Johann Wolfgang Goethe-University, Institute of Cell Biology and Neuroscience, Centre for Membrane Proteomics , Frankfurt am Main, Germany