Gisbert Schneider

Summary

Affiliation: F. Hoffmann-La Roche Ltd

Publications

  1. ncbi request reprint 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
  2. pmc Peptide design by artificial neural networks and computer-based evolutionary search
    G 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
  3. ncbi request reprint Virtual screening and fast automated docking methods
    Gisbert Schneider
    F Hoffmann La Roche, Pharmaceuticals Division, CH 4070 Basel, Switzerland
    Drug Discov Today 7:64-70. 2002
  4. ncbi request reprint Neural networks are useful tools for drug design
    G Schneider
    F Hoffmann La Roche Ltd, Pharmaceuticals Research, Basel, Switzerland
    Neural Netw 13:15-6. 2000
  5. ncbi request reprint De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
    G Schneider
    F Hoffmann La Roche Ltd, Pharmaceuticals Division, Basel, Switzerland
    J Comput Aided Mol Des 14:487-94. 2000
  6. ncbi request reprint Artificial neural networks for computer-based molecular design
    G Schneider
    F Hoffmann La Roche Ltd, Pharmaceuticals Division, Basel, Switzerland
    Prog Biophys Mol Biol 70:175-222. 1998
  7. ncbi request reprint Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using self-organizing maps
    Gisbert Schneider
    F Hoffmann La Roche AG, Pharmaceuticals Division, Lead Generation, Grenzacherstrasse 124, CH 4070 Basel, Switzerland
    J Comb Chem 5:233-7. 2003
  8. doi request reprint Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesity
    Leo Alig
    Pharmaceuticals Division, F Hoffmann La Roche Ltd, Basel, Switzerland
    J Med Chem 51:2115-27. 2008
  9. ncbi request reprint A virtual screening method for prediction of the HERG potassium channel liability of compound libraries
    Olivier Roche
    F Hoffmann La Roche AG, Pharmaceuticals Division, 4070 Basel, Switzerland
    Chembiochem 3:455-9. 2002
  10. ncbi request reprint Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening
    Steffen Renner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Marie Curie Strasse 11, D 60439 Frankfurt, Germany
    J Med Chem 47:4653-64. 2004

Collaborators

Detail Information

Publications32

  1. ncbi request reprint 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...
  2. pmc Peptide design by artificial neural networks and computer-based evolutionary search
    G 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...
  3. ncbi request reprint Virtual screening and fast automated docking methods
    Gisbert 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...
  4. ncbi request reprint Neural networks are useful tools for drug design
    G 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...
  5. ncbi request reprint De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
    G 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...
  6. ncbi request reprint Artificial neural networks for computer-based molecular design
    G 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...
  7. ncbi request reprint Ligand-based combinatorial design of selective purinergic receptor (A2A) antagonists using self-organizing maps
    Gisbert 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...
  8. doi request reprint Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesity
    Leo 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...
  9. ncbi request reprint A virtual screening method for prediction of the HERG potassium channel liability of compound libraries
    Olivier 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...
  10. ncbi request reprint Fuzzy pharmacophore models from molecular alignments for correlation-vector-based virtual screening
    Steffen Renner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, 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...
  11. ncbi request reprint A pseudo-ligand approach to virtual screening
    Andreas 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...
  12. ncbi request reprint NIPALSTREE: a new hierarchical clustering approach for large compound libraries and its application to virtual screening
    Alexander 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...
  13. ncbi request reprint Trends in virtual combinatorial library design
    Gisbert 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
    ....
  14. ncbi request reprint Impact of conformational flexibility on three-dimensional similarity searching using correlation vectors
    Steffen Renner
    Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, Siesmayerstrasse 70, D 60323 Frankfurt am Main, Germany
    J Chem Inf Model 46:2324-32. 2006
    ....
  15. ncbi request reprint Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo design
    Uli 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...
  16. ncbi request reprint Scaffold hopping by "fuzzy" pharmacophores and its application to RNA targets
    Yusuf Tanrikulu
    Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Siesmayerstrasse 70, 60323 Frankfurt am Main, Germany
    Chembiochem 8:1932-6. 2007
  17. ncbi request reprint The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA
    Andreas 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...
  18. doi request reprint Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization
    Markus 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...
  19. doi request reprint Identification of hits and lead structure candidates with limited resources by adaptive optimization
    Andreas 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...
  20. doi request reprint Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening
    Yusuf 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...
  21. ncbi request reprint Virtual screening for PPAR modulators using a probabilistic neural network
    Swetlana Derksen
    Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology ZAFES, Siesmayerstrasse 70, 60323 Frankfurt Main, Germany
    ChemMedChem 1:1346-50. 2006
  22. ncbi request reprint SOMMER: self-organising maps for education and research
    Michael 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...
  23. ncbi request reprint Impact of descriptor vector scaling on the classification of drugs and nondrugs with artificial neural networks
    Alireza 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...
  24. ncbi request reprint SVM-based feature selection for characterization of focused compound collections
    Evgeny Byvatov
    Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, 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...
  25. ncbi request reprint Impact of different software implementations on the performance of the Maxmin method for diverse subset selection
    Michael Schmuker
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, 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...
  26. ncbi request reprint New allosteric modulators of metabotropic glutamate receptor 5 (mGluR5) found by ligand-based virtual screening
    Steffen Renner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Marie Curie Strasse 11, 60439 Frankfurt am Main, Germany
    Chembiochem 6:620-5. 2005
  27. ncbi request reprint New inhibitors of the Tat-TAR RNA interaction found with a "fuzzy" pharmacophore model
    Steffen Renner
    Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, 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...
  28. ncbi request reprint A hierarchical clustering approach for large compound libraries
    Alexander 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)...
  29. ncbi request reprint Computer-based de novo design of drug-like molecules
    Gisbert 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...
  30. ncbi request reprint Flux (1): a virtual synthesis scheme for fragment-based de novo design
    Uli Fechner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, 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...
  31. ncbi request reprint Predicting compound selectivity by self-organizing maps: cross-activities of metabotropic glutamate receptor antagonists
    Tobias Noeske
    Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology ZAFES CMP, Siesmayerstr 70, Frankfurt, Germany
    ChemMedChem 1:1066-8. 2006
  32. doi request reprint Scaffold diversity of natural products: inspiration for combinatorial library design
    Kristina 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...