Gisbert Schneider

Summary

Country: Germany

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. ncbi request reprint Advances in the prediction of protein targeting signals
    Gisbert Schneider
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Frankfurt, Germany
    Proteomics 4:1571-80. 2004
  6. 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
  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. 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
  9. doi request reprint 2,4-Diaminopyrimidines as histamine H4 receptor ligands--Scaffold optimization and pharmacological characterization
    Kerstin Sander
    Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, ZAFES LiFF CMP, Max von Laue Str 9, 60438 Frankfurt Main, Germany
    Bioorg Med Chem 17:7186-96. 2009
  10. doi request reprint Form follows function: shape analysis of protein cavities for receptor-based drug design
    Martin Weisel
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Frankfurt am Main, Germany
    Proteomics 9:451-9. 2009

Collaborators

Detail Information

Publications67

  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. ncbi request reprint Advances in the prediction of protein targeting signals
    Gisbert Schneider
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Frankfurt, Germany
    Proteomics 4:1571-80. 2004
    ..Focus of the review is on machine learning systems, highlighting four concepts: the artificial neural feed-forward network, the self-organizing map (SOM), the Hidden-Markov-Model (HMM), and the support vector machine (SVM)...
  6. 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...
  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. 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...
  9. doi request reprint 2,4-Diaminopyrimidines as histamine H4 receptor ligands--Scaffold optimization and pharmacological characterization
    Kerstin Sander
    Johann Wolfgang Goethe University, Institute of Pharmaceutical Chemistry, ZAFES LiFF CMP, Max von Laue Str 9, 60438 Frankfurt Main, Germany
    Bioorg Med Chem 17:7186-96. 2009
    ....
  10. doi request reprint Form follows function: shape analysis of protein cavities for receptor-based drug design
    Martin Weisel
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Frankfurt am Main, Germany
    Proteomics 9:451-9. 2009
    ..The new method provides a means for selecting drug targets and potential ligand-binding pockets based on structural considerations and addresses orphan binding sites...
  11. 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
  12. doi request reprint Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists
    Bjoern A Krueger
    Institute of Organic Chemistry und Chemical Biology, Johann Wolfgang Goethe University, 60323 Frankfurt, Germany
    J Comput Aided Mol Des 23:869-81. 2009
    ....
  13. doi request reprint Homology model adjustment and ligand screening with a pseudoreceptor of the human histamine H4 receptor
    Yusuf Tanrikulu
    Chem and Bioinformatics LiFF ZAFES CMP, Johann Wolfgang Goethe University, Siesmayerstr 70, 60323 Frankfurt a M, Germany
    ChemMedChem 4:820-7. 2009
    ..This new pseudoreceptor approach has demonstrated its suitability for both structure-based prioritization of protein receptor models, and ligand-based virtual screening with the aim to perform scaffold hopping...
  14. 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
  15. doi request reprint Structure-activity relationship of nonacidic quinazolinone inhibitors of human microsomal prostaglandin synthase 1 (mPGES 1)
    Florian Rörsch
    Johann Wolfgang Goethe University, Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, LiFF ZAFES, Theodor Stern Kai 7, D 60590 Frankfurt Main, Germany
    J Med Chem 55:3792-803. 2012
    ..Furthermore, pharmacological profiling of toxicity and eicosanoid screening with LC/MS-MS was applied to characterize this new class of mPGES-1 inhibitors...
  16. ncbi request reprint Fate of primary cells at the G₁/S boundary after polo-like kinase 1 inhibition by SBE13
    Sarah Keppner
    Department of Obstetrics and Gynecology, Medical School, Goethe University, Frankfurt, Germany
    Cell Cycle 10:708-20. 2011
    ..Thus, we provide strong evidence that SBE13 leaves checkpoint control in primary cells unaffected making it a remarkable future anti-cancer therapeutic...
  17. 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...
  18. pmc Spherical harmonics coefficients for ligand-based virtual screening of cyclooxygenase inhibitors
    Quan Wang
    Frankfurt Institute for Advanced Studies, Goethe University, Frankfurt, Germany
    PLoS ONE 6:e21554. 2011
    ..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...
  19. doi request reprint Nonacidic inhibitors of human microsomal prostaglandin synthase 1 (mPGES 1) identified by a multistep virtual screening protocol
    Florian Rörsch
    Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, LiFF ZAFES, Siesmayer Strasse 70 B, D 60323 Frankfurt Main, Germany
    J Med Chem 53:911-5. 2010
    ..Here, we present a successful virtual screening study that results in a potent nonacidic mPGES-1 inhibitor lacking COX inhibition...
  20. pmc Inhibitors of Helicobacter pylori protease HtrA found by 'virtual ligand' screening combat bacterial invasion of epithelia
    Martin Löwer
    Institute of Organic Chemistry and Chemical Biology, Goethe University, Frankfurt, Germany
    PLoS ONE 6:e17986. 2011
    ..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...
  21. doi request reprint Protein-protein docking by shape-complementarity and property matching
    Tim Geppert
    Department of Biochemistry, Chemistry and Pharmacy, Institute of Organic Chemistry and Chemical Biology, LiFF ZAFES, Johann Wolfgang Goethe University, Frankfurt am Main, Germany
    J Comput Chem 31:1919-28. 2010
    ..In 82% of the unbound samples, docking poses were ranked within the top ten solutions with an RMSD < 10 A to the target solution...
  22. ncbi request reprint Scaffold-hopping potential of fragment-based de novo design: the chances and limits of variation
    Bjoern A Krueger
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Siesmayerstrasse 70, Frankfurt am Main, Germany
    Comb Chem High Throughput Screen 12:383-96. 2009
    ..We demonstrate that for one or multiple templates of a given chemotype, other chemotypes are reached during de novo compound generation, thus indicating successful scaffold-hops...
  23. ncbi request reprint Molecular query language (MQL)--a context-free grammar for substructure matching
    Ewgenij Proschak
    Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Chair for Chem and Bioinformatics, Siesmayerstrasse 70, D 60323 Frankfurt am Main, Germany
    J Chem Inf Model 47:295-301. 2007
    ..We already implemented these interfaces for the Chemistry Development Toolkit...
  24. doi request reprint Architectural repertoire of ligand-binding pockets on protein surfaces
    Martin Weisel
    Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Siesmayerstr 70, 60323 Frankfurt am Main, Germany
    Chembiochem 11:556-63. 2010
    ..Pocket frameworks highlight potentially preferred modes of ligand-receptor interactions and will help facilitate the identification of druggable subpockets suitable for ligand affinity and selectivity optimization...
  25. doi request reprint Voyages to the (un)known: adaptive design of bioactive compounds
    Gisbert Schneider
    Johann Wolfgang Goethe University, Institute of Organic Chemistry and Chemical Biology, Liff, Siesmayerstr 70, D 60323 Frankfurt am Main, Germany
    Trends Biotechnol 27:18-26. 2009
    ..Evolving compound libraries are particularly suited for hit and lead finding in situations where resources are limited and the complete testing of a large screening compound collection is prohibitive...
  26. 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...
  27. doi request reprint Distance phenomena in high-dimensional chemical descriptor spaces: consequences for similarity-based approaches
    Matthias Rupp
    Johann Wolfgang Goethe University, Siesmayerstrasse 70, 60323 Frankfurt am Main, Germany
    J Comput Chem 30:2285-96. 2009
    ..These phenomena are theoretically characterized and illustrated on both artificial and real (bioactivity) data...
  28. doi request reprint Self-organizing molecular fingerprints: a ligand-based view on drug-like chemical space and off-target prediction
    Gisbert Schneider
    Johann Wolfgang Goethe University, Siesmayerstr 70, D 60323 Frankfurt am Main, Germany
    Future Med Chem 1:213-8. 2009
    ..We developed a ligand-based computational method for drug-target prediction that is independent from protein structural analysis...
  29. doi request reprint De novo drug design
    Markus Hartenfeller
    Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Frankfurt, Germany
    Methods Mol Biol 672:299-323. 2011
    ..Recent practical validation studies are presented that have already demonstrated that rule-based fragment assembly can result in novel synthesizable compounds with druglike properties and a desired biological activity...
  30. 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...
  31. 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...
  32. doi request reprint Prediction of turn types in protein structure by machine-learning classifiers
    Michael Meissner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie and Chemische Biologie, Siesmayerstr 70, D 60323 Frankfurt am Main, Germany
    Proteins 74:344-52. 2009
    ..Their potential for sequence-based prediction of turn structures is discussed...
  33. 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
  34. ncbi request reprint Identification of natural-product-derived inhibitors of 5-lipoxygenase activity by ligand-based virtual screening
    Lutz Franke
    Institut für Organische Chemie und Chemische Biologie ZAFES, Johann Wolfgang Goethe Universitat, Siesmayerstrasse 70, D 60323 Frankfurt am Main, Germany
    J Med Chem 50:2640-6. 2007
    ..The results demonstrate the potential of natural-product-derived screening libraries for hit and lead structure identification...
  35. pmc Prediction of type III secretion signals in genomes of gram-negative bacteria
    Martin Löwer
    Johann Wolfgang Goethe University, Chair for Chem and Bioinformatics, Frankfurt, Germany
    PLoS ONE 4:e5917. 2009
    ..Although a special targeting signal at the N-terminal end of effector proteins has been proposed in literature its exact characteristics remain unknown...
  36. doi request reprint Pharmacophore alignment search tool: Influence of canonical atom labeling on similarity searching
    Volker Hähnke
    Johann Wolfgang Goethe University, Frankfurt am Main 60323, Germany
    J Comput Chem 31:2810-26. 2010
    ..Finally, we introduce a performance index that helps prioritize canonization approaches without the need for extensive retrospective evaluation...
  37. ncbi request reprint Scaffold-hopping potential of ligand-based similarity concepts
    Steffen Renner
    Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Siesmayerstrasse 70, 60323 Frankfurt, Germany
    ChemMedChem 1:181-5. 2006
  38. 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)...
  39. doi request reprint Adaptive combinatorial design of focused compound libraries
    Gisbert Schneider
    Institute of Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main, Germany
    Methods Mol Biol 572:135-47. 2009
    ..We show that there exists an optimal combination of the size of a screening library and the number of iterative screening rounds with the aim to keep experimental efforts at a minimum...
  40. ncbi request reprint Kernel approach to molecular similarity based on iterative graph similarity
    Matthias Rupp
    Johann Wolfgang Goethe University, Siesmayerstrasse 70, Frankfurt am Main, Germany
    J Chem Inf Model 47:2280-6. 2007
    ..We evaluated our molecular similarity measure by using it as a kernel in support vector machine classification and regression applied to several pharmaceutical and toxicological data sets, with encouraging results...
  41. 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...
  42. ncbi request reprint Support vector machine applications in bioinformatics
    Evgeny Byvatov
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Frankfurt, Germany
    Appl Bioinformatics 2:67-77. 2003
    ..78. This classifier can be used for fast filtering of compound libraries in virtual screening applications...
  43. pmc Processing and classification of chemical data inspired by insect olfaction
    Michael Schmuker
    Beilstein Endowed Chair for Cheminformatics, Johann Wolfgang Goethe Universitat, Siesmayerstrasse 70, 60323 Frankfurt, Germany
    Proc Natl Acad Sci U S A 104:20285-9. 2007
    ..Our olfaction-inspired method was successfully applied to predicting bioactivities of pharmaceutically active compounds with high accuracy. It represents a way to efficiently connect chemical structure with biological activity space...
  44. pmc The Plasmodium export element revisited
    Jan Alexander Hiss
    Johann Wolfgang Goethe University, Institute of Cell Biology and Neuroscience, Centre for Membrane Proteomics, Frankfurt am Main, Germany
    PLoS ONE 3:e1560. 2008
    ..We further show that signal peptide cleavage results in a positional alignment of PEXEL from both proteins with, and without, a signal peptide...
  45. ncbi request reprint Multi-space classification for predicting GPCR-ligands
    Alireza Givehchi
    Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, Marie Curie Strasse 11, D 60439, Frankfurt, Germany
    Mol Divers 9:371-83. 2005
    ..Seventy-one percent correct prediction of GPCR ligands was obtained...
  46. doi request reprint Architecture, function and prediction of long signal peptides
    Jan A Hiss
    Johann Wolfgang Goethe University, D 60323 Frankfurt am Main, Germany
    Brief Bioinform 10:569-78. 2009
    ..This concept provides a structural framework for identifying and understanding multiple targeting and post-targeting functions...
  47. 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...
  48. 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...
  49. 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
    ....
  50. pmc Optimized Particle Swarm Optimization (OPSO) and its application to artificial neural network training
    Michael Meissner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Siesmayerstrasse 70, D 60323 Frankfurt, Germany
    BMC Bioinformatics 7:125. 2006
    ..We assessed the performance of the OPSO method on a set of five artificial fitness functions and compared it to the performance of two popular PSO implementations...
  51. doi request reprint Identification of human cathepsin G as a functional target of boswellic acids from the anti-inflammatory remedy frankincense
    Lars Tausch
    Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
    J Immunol 183:3433-42. 2009
    ..In conclusion, we show that catG is a functional and pharmacologically relevant target of BAs, and interference with catG could explain some of the anti-inflammatory properties of frankincense...
  52. ncbi request reprint Biological impact of freezing Plk1 in its inactive conformation in cancer cells
    Sarah Keppner
    Department of Obstetrics and Gynecology, Medical School, Goethe University, Frankfurt, Germany
    Cell Cycle 9:761-73. 2010
    ..This study suggests that Plk1 kinase inhibitors targeting the inactive conformation of Plk1 may be considered for the development of cancer therapeutics...
  53. 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...
  54. pmc MHC I stabilizing potential of computer-designed octapeptides
    Joanna M Wisniewska
    Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe Universitat, Siesmayerstrasse 70, 60323 Frankfurt am Main, Germany
    J Biomed Biotechnol 2010:396847. 2010
    ..The experimental results present evidence that the canonical sequence motives of the SYFPEITHI database on their own are insufficient for predicting MHC I protein stabilization...
  55. ncbi request reprint Comparison of support vector machine and artificial neural network systems for drug/nondrug classification
    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 43:1882-9. 2003
    ..The theory of SVM and ANN training is briefly reviewed...
  56. ncbi request reprint Evaluation of distance metrics for ligand-based similarity searching
    Uli Fechner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Marie Curie Strasse 11, 60439 Frankfurt, Germany
    Chembiochem 5:538-40. 2004
  57. 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...
  58. 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...
  59. 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
  60. 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...
  61. 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
    ....
  62. pmc Domain organization of long signal peptides of single-pass integral membrane proteins reveals multiple functional capacity
    Jan A Hiss
    Centre for Membrane Proteomics, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt am Main, Germany
    PLoS ONE 3:e2767. 2008
    ....
  63. ncbi request reprint Extraction and visualization of potential pharmacophore points using support vector machines: application to ligand-based virtual screening for COX-2 inhibitors
    Lutz Franke
    Institut für Organische Chemie und Chemische Biologie and Institut für Pharmazeutische Chemie, Johann Wolfgang Goethe Universitat, Marie Curie Strasse 9, D 60439 Frankfurt, Germany
    J Med Chem 48:6997-7004. 2005
    ..It was demonstrated that the SVM machine-learning method can be used in virtual screening and be analyzed in a human-interpretable way that results in a set of rules for designing novel molecules...
  64. ncbi request reprint Comparison of correlation vector methods for ligand-based similarity searching
    Uli Fechner
    Johann Wolfgang Goethe Universitat, Institut für Organische Chemie und Chemische Biologie, Marie Curie Str 11, D 60439 Frankfurt, Germany
    J Comput Aided Mol Des 17:687-98. 2003
    ..The suitability of a descriptor critically depends on the ligand-receptor interaction under investigation. For ligand-based similarity searching it is recommended to exploit several descriptors in parallel...
  65. ncbi request reprint Development of a virtual screening method for identification of "frequent hitters" in compound libraries
    Olivier Roche
    F Hoffmann La Roche AG, CH 4070 Basel, Switzerland
    J Med Chem 45:137-42. 2002
    ..This filter will be a valuable tool for the prioritization of compounds from large databases, for compound purchase and biological testing, and for building new virtual libraries...
  66. ncbi request reprint From virtual to real screening for D3 dopamine receptor ligands
    Evgeny Byvatov
    Fachbereich Chemische und Pharmazeutische Wissenschaften, Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe Universitat, Marie Curie Strasse 11, 60439 Frankfurt am Main, Germany
    Chembiochem 6:997-9. 2005
  67. 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...