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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 ...

Bioassays to Monitor Taspase1 Function for the Identification of Pharmacogenetic Inhibitors

Background Threonine Aspartase 1 (Taspase1) mediates cleavage of the mixed lineage leukemia (MLL) protein and leukemia provoking MLL-fusions. In contrast to other proteases, the understanding of Taspase1's (patho)biological relevance and function is limited, since neither small molecule inhibitors nor cell based functional assays for Taspase1 are currently available. ...

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 ...

Design of MHC I stabilizing peptides by agent-based exploration of sequence space

Identification of molecular features that determine peptide interaction with major histocompatibility complex I (MHC I) is essential for vaccine development. We have developed a concept for peptide design by combining an agent-based artificial ant system with artificial neural networks. A jury of feedforward networks classifies octapeptides that are recognized by mouse MHC I ...

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. ...

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 ...

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

Local structural motifs of protein backbones are classified by self-organizing neural networks

Important and relevant information is expected to be encoded in local structural elements of proteins. An unsupervised learning algorithm (Kohonen algorithm) was applied to the representation and unbiased classification of local backbone structures contained in a set of proteins. Training yielded a two-dimensional Kohonen feature map with 100 different structural motifs including ...

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. ...

Mapping of protein surface cavities and prediction of enzyme class by a self-organizing neural network

Martin Stahl 0 Chiara Taroni 0 Gisbert Schneider 0 0 F.Hoffmann-La Roche Ltd, Pharmaceuticals Research , CH-4070 Basel , Switzerland 1To whom correspondence should be addressed; email: An automated

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

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 ...

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 ...

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 ...