Research Topics
| Gisbert SchneiderSummaryAffiliation: F. Hoffmann-La Roche Ltd Publications
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Detail Information
Publications
How many potentially secreted proteins are contained in a bacterial genome?G Schneider
F Hoffmann La Roche Ltd, Pharmaceuticals Division, Basel, Switzerland
Gene 237:113-21. 1999..The Treponema pallidum and Mycobacterium tuberculosis data formed separate clusters indicating unusual characteristics of these genomes...
Peptide design by artificial neural networks and computer-based evolutionary searchG Schneider
Freie Universitat Berlin, Universitatsklinikum Benjamin Franklin, Institut für Medizinische Technische Physik und Lasermedizin, Krahmerstrasse 6 10, D 12207 Berlin, Germany
Proc Natl Acad Sci U S A 95:12179-84. 1998..De novo design revealed peptides with desired activities that do not match the seed peptide sequence. These results demonstrate that computer-based evolutionary searches can generate novel peptides with substantial biological activity...- Virtual screening and fast automated docking methodsGisbert Schneider
F Hoffmann La Roche, Pharmaceuticals Division, CH 4070 Basel, Switzerland
Drug Discov Today 7:64-70. 2002..This review provides a brief introduction to the basic ideas and outlines computational tools currently used. We also provide several examples of where virtual screening has proved successful, highlighting the usefulness of the approach... - Neural networks are useful tools for drug designG Schneider
F Hoffmann La Roche Ltd, Pharmaceuticals Research, Basel, Switzerland
Neural Netw 13:15-6. 2000..Neural networks could play an important role in guiding the Drug Discovery process through the extraction of relevant molecular features... - De novo design of molecular architectures by evolutionary assembly of drug-derived building blocksG Schneider
F Hoffmann La Roche Ltd, Pharmaceuticals Division, Basel, Switzerland
J Comput Aided Mol Des 14:487-94. 2000..The efficiency of the design algorithm was demonstrated for the de novo construction of potential thrombin inhibitors mimicking peptide and non-peptide template structures... - Artificial neural networks for computer-based molecular designG Schneider
F Hoffmann La Roche Ltd, Pharmaceuticals Division, Basel, Switzerland
Prog Biophys Mol Biol 70:175-222. 1998..Advantages and limitations of neural networks for computer-aided molecular design and sequence analysis are discussed... - Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using self-organizing mapsGisbert Schneider
F Hoffmann La Roche AG, Pharmaceuticals Division, Lead Generation, Grenzacherstrasse 124, CH 4070 Basel, Switzerland
J Comb Chem 5:233-7. 2003..The strategy might be particularly useful in projects in which structure-based design cannot be applied because of a lack of receptor structure information, for example, in the many projects aiming at finding new GPCR modulators... 
Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesityLeo Alig
Pharmaceuticals Division, F Hoffmann La Roche Ltd, Basel, Switzerland
J Med Chem 51:2115-27. 2008..Biochemical, pharmacokinetic, and pharmacodynamic characteristics of ( R)-14g are discussed...- A virtual screening method for prediction of the HERG potassium channel liability of compound librariesOlivier Roche
F. Hoffmann-La Roche AG, Pharmaceuticals Division, 4070 Basel, Switzerland
Chembiochem 3:455-9. 2002..In a validation study, 93 % of the nonblocking agents and 71 % of the hERG channel blockers were correctly classified. This virtual screening method can be used for general compound-library shaping and combinatorial library design... - Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screeningSteffen Renner
, , Marie-Curie-Strasse 11, D-60439 Frankfurt, Germany
J Med Chem 47:4653-64. 2004..Appropriately weighted fuzzy pharmacophore models performed better in retrospective screening than similarity searching using only a single query molecule. The new pharmacophore method was shown to complement existing approaches... - A pseudo-ligand approach to virtual screeningAndreas Schüller
Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Siesmayerstr 70, D 60323 Frankfurt am Main, Germany
Comb Chem High Throughput Screen 9:359-64. 2006..The approach provides a concept for "de-orphanizing" potential drug targets and identifying ligands for hitherto unexplored or allosteric binding pockets... - NIPALSTREE: a new hierarchical clustering approach for large compound libraries and its application to virtual screeningAlexander Böcker
Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, Marie Curie Strasse 11, D 60439 Frankfurt, Germany
J Chem Inf Model 46:2220-9. 2006..Results show that both algorithms can be used in the context of virtual screening. Intersecting the result lists obtained with both algorithms improved enrichment factors while losing only few chemotypes... - Trends in virtual combinatorial library designGisbert Schneider
Johann Wolfgang Goethe Universitat, Beilstein Professor of Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Marie Curie Str, Frankfurt, 11, D 60439, Germany
Curr Med Chem 9:2095-101. 2002.... - Impact of conformational flexibility on three-dimensional similarity searching using correlation vectorsSteffen Renner
, , Siesmayerstrasse 70, D-60323 Frankfurt am Main, Germany
J Chem Inf Model 46:2324-32. 2006.... - Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo designUli Fechner
Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Siesmeyerstrasse 70, D 60323 Frankfurt am Main, Germany
J Chem Inf Model 47:656-67. 2007..We conclude that this fragment-based design principle is suited as an idea generator for the automated design of novel leadlike molecules... - Scaffold hopping by "fuzzy" pharmacophores and its application to RNA targetsYusuf Tanrikulu
Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Siesmayerstrasse 70, 60323 Frankfurt am Main, Germany
Chembiochem 8:1932-6. 2007 - The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNAAndreas Schüller
Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max von Laue Strasse 7, Chair for Chem and Bioinformatics Siesmayerstr 70, 60323 Frankfurt am Main, Germany
J Comput Aided Mol Des 22:59-68. 2008..Chemical synthesis was straightforward, and bioactivity of the designed molecule was confirmed in a FRET assay. This study demonstrates the practicability of de novo design to generating RNA ligands containing novel molecular scaffolds... - Concept of combinatorial de novo design of drug-like molecules by particle swarm optimizationMarkus Hartenfeller
Institute of Organic Chemistry and Chemical Biology ZAFES, CMP, Goethe University, Siesmayerstr 70, D 60323 Frankfurt a M, Germany
Chem Biol Drug Des 72:16-26. 2008..It thereby represents a practical solution for compound screening in the early hit and lead finding phase of a drug discovery project... - Identification of hits and lead structure candidates with limited resources by adaptive optimizationAndreas Schüller
Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Siesmayerstrasse 70, 60323 Frankfurt, Germany
J Chem Inf Model 48:1473-91. 2008..We further demonstrate that a nearest neighbor algorithm can successfully be applied to map from continuous search space to discrete chemical space... - Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screeningYusuf Tanrikulu
Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Siesmayerstrasse 70, D 60323 Frankfurt, Germany
Nat Rev Drug Discov 7:667-77. 2008..Here, we review the field of pseudoreceptor modelling techniques along with recent hit and lead finding applications, and critically discuss prerequisites, advantages and limitations of the various approaches... - Virtual screening for PPAR modulators using a probabilistic neural networkSwetlana Derksen
Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology/ZAFES, Siesmayerstrasse 70, 60323 Frankfurt/Main, Germany
ChemMedChem 1:1346-50. 2006 - SOMMER: self-organising maps for education and researchMichael Schmuker
Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Siesmayerstr 70, 60323, Frankfurt, Germany
J Mol Model 13:225-8. 2007..The software allows for visualization of the training process, which has been shown to be particularly valuable for teaching purposes... - Impact of descriptor vector scaling on the classification of drugs and nondrugs with artificial neural networksAlireza Givehchi
Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, Marie Curie Str 11, 60439 Frankfurt, Germany
J Mol Model 10:204-11. 2004..The results demonstrate that appropriate data preprocessing is an essential step in solving classification tasks... - SVM-based feature selection for characterization of focused compound collectionsEvgeny Byvatov
, , Marie-Curie-Strasse 11, D-60439 Frankfurt, Germany
J Chem Inf Comput Sci 44:993-9. 2004..In one case both methods produced comparable results. Limiting the calculation of descriptors to only the most relevant ones for a certain biological activity can also be used to speed up high-throughput virtual screening... - Impact of different software implementations on the performance of the Maxmin method for diverse subset selectionMichael Schmuker
, , Marie-Curie-Str 11, D-60439 Frankfurt, Germany
Mol Divers 8:421-5. 2004..While the Java version selects the same compounds independent of the virtual machine used, the C version produces slightly different subsets depending on the compiler and on the optimization settings... - New allosteric modulators of metabotropic glutamate receptor 5 (mGluR5) found by ligand-based virtual screeningSteffen Renner
, , Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
Chembiochem 6:620-5. 2005 - New inhibitors of the Tat-TAR RNA interaction found with a "fuzzy" pharmacophore modelSteffen Renner
Beilstein Endowed Chair for Cheminformatics, , , Marie-Curie-Strasse 11, 60439 Frankfurt am Main, Germany
Chembiochem 6:1119-25. 2005..The hits had molecular scaffolds different from those of the reference molecules... - A hierarchical clustering approach for large compound librariesAlexander Böcker
Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Marie Curie Str 11, D 60439 Frankfurt, Germany
J Chem Inf Model 45:807-15. 2005..A Java implementation of the clustering method is available via the Internet (http://www.modlab.de)... - Computer-based de novo design of drug-like moleculesGisbert Schneider
Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Marie Curie Str 11 D 60439 Frankfurt am Main, Germany
Nat Rev Drug Discov 4:649-63. 2005..In this review, we outline the various design concepts and highlight current developments in computer-based de novo design... - Flux (1): a virtual synthesis scheme for fragment-based de novo designUli Fechner
, , Marie-Curie-Str. 11, D-60439 Frankfurt, Germany
J Chem Inf Model 46:699-707. 2006..A comparison of molecular descriptors suggests that holographic descriptors might be advantageous over binary fingerprints for ligand-based de novo design... - Predicting compound selectivity by self-organizing maps: cross-activities of metabotropic glutamate receptor antagonistsTobias Noeske
Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology ZAFES/CMP, Siesmayerstr 70, Frankfurt, Germany
ChemMedChem 1:1066-8. 2006 - Scaffold diversity of natural products: inspiration for combinatorial library designKristina Grabowski
Institute of Organic Chemistry and Chemical Biology, ZAFES CMP, Goethe University, Siesmayerstrasse 70, Frankfurt a M, Germany
Nat Prod Rep 25:892-904. 2008..In particular, an application of the self-organizing map technique is presented for natural product-derived compound and library design...