Tim Geppert

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BACKGROUND The human pathogen Helicobacter pylori (H. pylori) is a main cause for gastric inflammation and cancer. Increasing bacterial resistance against antibiotics demands for innovative strategies for therapeutic intervention. METHODOLOGY/PRINCIPAL FINDINGS We present a method for structure-based virtual screening that is based on the comprehensive(More)
We present a computational approach to protein-protein docking based on surface shape complementarity ("ProBinder"). Within this docking approach, we implemented a new surface decomposition method that considers local shape features on the protein surface. This new surface shape decomposition results in a deterministic representation of curvature features(More)
We present the discovery of low molecular weight inhibitors of human immunodeficiency virus 1 (HIV-1) protease subtype B that were identified by structure-based virtual screening as ligands of an allosteric surface cavity. For pocket identification and prioritization, we performed a molecular dynamics simulation and observed several flexible, partially(More)
Within this work, a methodological extension of the matched molecular pair analysis is presented. The method is based on a pharmacophore retyping of the molecular graph and a consecutive matched molecular pair analysis. The features of the new methodology are exemplified using a large data set on CYP inhibition. We show that Fuzzy Matched Pairs can be used(More)
Joint design and load transmission are crucial factors when building autonomous robots. On the one hand, heavy torques are often needed which result in multi-stage gearboxes, on the other hand the latter exhibit massive friction which gets in the way of energy-efficient ac-tuation systems. Furthermore, the immense impact forces of a tumbling robot can(More)
Modulation of protein-protein interactions (PPI) has emerged as a new concept in rational drug design. Here, we present a computational protocol for identifying potential PPI inhibitors. Relevant regions of interfaces (epitopes) are predicted for three-dimensional protein models and serve as queries for virtual compound screening. We present a computational(More)
For the development of robots the mode of assembly and the effectiveness of their joints are of elementary significance. To enable powerful movements, strong torques are required which, when employing electromechanical actuators, are generated by high-capacity motors in combination with adequate speed transformations. Furthermore, such drive systems have to(More)
We have recently demonstrated that Taspase1-mediated cleavage of the AF4-MLL oncoprotein results in the formation of a stable multiprotein complex which forms the key event for the onset of acute proB leukemia in mice. Therefore, Taspase1 represents a conditional oncoprotein in the context of t(4;11) leukemia. In this report, we used site-directed(More)
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. (More)
We present a self-organizing map (SOM) approach to predicting macromolecular targets for combinatorial compound libraries. The aim was to study the usefulness of the SOM in combination with a topological pharmacophore representation (CATS) for selecting biologically active compounds from a virtual combinatorial compound collection, taking the(More)
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