Publications

Gisbert Schneider is Co-editor of the journal Molecular Informatics. He acts as Senior Honorary Advisor to Chemistry Central Journal, and is a member of the Editorial Advisory Boards of ChemBioChem, Current Chemical Biology, Future Medicinal Chemistry, Molecules, and the Journal of Molecular Modeling.

2012

• Fjell, C. D., Hiss, J. A., Hancock, R. E. W. and Schneider, G. (2012) Designing antimicrobial peptides: Form follows function. Nat. Rev. Drug Discov. 11, 37-51.
• Geppert, T., Bauer, S., Hiss, J. A., Conrad, E., Reutlinger, M., Schneider, P., Weisel, M., Pfeiffer, B., Altmann, K. H., Waibler, Z. and Schneider, G. (2012) Immunosuppressive small molecule discovered by structure-based virtual screening for protein-protein interaction inhibitors. Angew. Chem. Int. Ed. 51, 258-261.
• Hartenfeller, M., Zettl, H., Walter, M., Rupp, M., Reisen, F., Proschak, E., Weggen, S., Stark, H. and Schneider, G. (2012) DOGS: Reaction-driven de novo design of bioactive compounds. PLoS Comput. Biol. 8, e1002380.
• Klenner, A., Hähnke, V., Geppert, T., Schneider, P., Zettl, H., Haller, S., Rodrigues, T., Reisen, F., Hoy, B., Schaible, A. M., Werz, O., Wessler, S. and Schneider, G. (2012) From virtual screening to bioactive compounds by visualizing and clustering of chemical space. Mol. Inf. 31, 21-26.
• Schneider, G. (2012) Designing the molecular future. J. Comput. Aided Mol. Des. 26, 115-120.
• Geppert, T., Reisen, F., Pillong, M., Hähnke, V., Tanrikulu, Y., Koch, C. P., Perna, A. M., Perez T. B., Schneider, P. and Schneider, G. (2012) Virtual screening for compounds that mimic protein-protein interface epitopes. J. Comput. Chem. 33, 573-579.
• Reutlinger, M. and Schneider, G. (2012) Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery. J. Mol. Graphics Modell. 34, 108-117.
• Schneider, G. (2012) From theory to bench experiment by computer-assisted drug design. Chimia 66, 120-124.
• Hofmann, B., Rödl, C. B., Fischer, A. S. Maier, T. J., Michel, A. A., Hoffmann, A., Rau, O., Awwad, K., Pellowska, M., Wurglics, M., Wacker, M., Zivkovic, A., Fleming, I., Schubert-Zsilavecz, M., Stark, H., Schneider, G. and Steinhilber, D. (2012) Molecular pharmacological profile of a novel thiazolinone-based direct and selective 5-lipoxygenase inhibitor. Brit. J. Pharmacol. 165, 2304-2313.
• Winiewska, J. M., Rödl, C. B., Kahn, A. S., Ulrich, S., Tanrikulu, Y., Achenbach, J., Rörsch, F., Grösch, S., Schneider, G., Cinatl Jr., J., Proschak, E., Steinhilber, D. and Hofmann, B. (2012) Molecular characterization of EP6 - a novel imidazo[1,2-a]pyridine based direct 5-lipoxygenase inhibitor. Biochem. Pharmacol. 83, 228-240.
• Hoy, B., Geppert, T., Boehm, M. Reisen, F., Plattner, P., Gademaier, G., Sewald, N., Ferreira, F., Briza, P., Schneider, G., Backert, S. and Wessler, S. (2012) Distinct roles of secreted HtrA proteases from Gram-negative pathogens in cleaving the junctional protein and tumor suppressor E-cadherin. J. Biol. Chem. 287, 10115-10120.
• Rörsch, F., La Buscato, E., Deckmann, K., Schneider, G., Schubert-Zsilavecz, M., Geisslinger, G., Proschak, E. and Grösch, S. (2012) Structure-activity relationship of non-acidic quinazolinone inhibitors of human microsomal prstaglandin synthase I (mPGES1). J. Med. Chem., accepted.
• Hartenfeller, M., Eberle, M., Meier, P., Nieto-Oberhuber, C., Altmann, K.-H., Schneider, G., Jacoby, E. and Renner, S. (2012) Probing the bioactivity-relevant chemical space of robust reactions and common molecular building blocks. J. Chem. Inf. Model., accepted.
  
• Meanwell, N. A., Gastreich, M., Rarey, M., Devereux, M., Popelier, P. L. A., Schneider, G. and Willett, P. (2012) Perspectives from Medicinal Chemistry. In: Bioisosters in Medicinal Chemistry (N. Brown, Ed.), Wiley-VCH, Weinheim, accepted.
• Reisen, F. and Schneider, G. (2012) Computational analysis of ligand binding pockets. In: Computational Chemogenomics (S. Chong, E. Jacoby, Eds), Pan Stanford Publishing, Singapore, accepted.
  

2011

• Reutlinger, M., Guba, W., Martin, R. E., Alanine, A. I., Hoffmann, T., Klenner, A., Hiss, J. A., Schneider, P. and Schneider, G. (2011) Neighborhood-preserving visualization of adaptive structure-activity landscapes and application to drug discovery. Angew. Chem. Int. Ed. 50, 11633-11636.
• Geppert, T., Hoy, B., Wessler, S. and Schneider, G. (2011) Context-based identification of protein-protein interfaces and 'hot-spot' residues. Chem. Biol. 18, 344-353.
• Hartenfeller, M. and Schneider, G. (2011) De novo drug design. Methods Mol. Biol. 672, 299-323.
• Schneider, G., Geppert, T., Hartenfeller, M., Reisen, F., Klenner, A., Reutlinger, M., Hähnke, V., Hiss, J. A., Zettl, H., Keppner, S., Spänkuch, S. and Schneider, P. (2011) Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors. Future Med. Chem. 3, 415-424.
• Hartenfeller, M. and Schneider, G. (2011) Enabling future drug discovery by de novo design. WIREs Comp. Mol. Sci. 1, 742-759.
• Urbanek, D. A., Proschak, E., Tanrikulu, Y., Becker, S., Karas, M. and Schneider, G. (2011) Scaffold-hopping from aminoglycosides to small synthetic inhibitors of bacterial protein biosynthesis using a pseudoreceptor model. Med. Chem. Commun. 2, 181-184.
• Bieler, M., Heilker, R., Koeppen, H. and Schneider, G. (2011) Assay related target similarity (ARTS) - Chemogenomics approach for quantitative comparison of biological targets. J. Chem. Inf. Model. 51, 1897-1905.
• Löwer, M., Geppert, T., Schneider, P., Hoy, B. Wessler, S. and Schneider, G. (2011) Inhibitors of Helicobacter pylori protease HtrA found by 'virtual ligand' screening combat bacterial invasion of epithelia. PLoS ONE 6, e17986.
• Hähnke, V., Klenner, A., Rippmann, F. and Schneider, G. (2011) Pharmacophore Alignment Search Tool: Influence of the third dimension on text-based similarity searching. J. Comput. Chem. 32, 1618-1634.
• Hähnke, V. and Schneider, G. (2011) Pharmacophore Alignment Search Tool: Influence of scoring systems on text-based similarity searching. J. Comput. Chem. 32, 1635-1647.
• Wang, Q., Birod, K., Angioni, C., Grösch, S., Geppert, T., Schneider, P., Rupp, M. and Schneider, G. (2011) Spherical harmonics coeffcients for ligand-based virtual screening of cyclooxygenase inhibitors. PLoS ONE 6, e21554.
• Schneider, P., Stutz, K., Kasper, L., Haller, S., Reutlinger, M., Reisen, F., Geppert, T. and Schneider, G. (2011) Target profile prediction for a Biginelli-type dihydropyrimidine compound library and practical evaluation. Pharmaceuticals 4, 1236-1247.
• Häfner, A. K., Cernescu, M., Hofmann, B., Ermisch, M., Hörnig, M., Metzner, J., Schneider, G., Brutschi, B. and Steinhilber, D. (2011) Dimerization of human 5-lipoxygenase. Biol. Chem. 392, 1097-1111.
• Resch, E., Hiss, J. A., Schreiner, A., Schneider, G. and Starzinski-Powitz, A. (2011) Long signal peptides of RGMa and DCBLD2 are dissectable into subdomains according to the NtraC model. Mol. Biosyst. 7, 942-951.
• Hofmann, B., Barzen, S., Rödl, C. B., Kiehl, A., Borig J., Zivkovic, A., Stark, H., Schneider, G. and Steinhilber, D. (2011) A class of 5-benzylidene-2-phenyl-thiazolinones with high potency as direct 5-lipoxygenase inhibitors. J. Med. Chem. 54, 1943-1947.
• Keppner, S., Proschak, E., Schneider, G. and Spänkuch, B. (2011) Fate of primary cells at the G1/S boundary after polo-like kinase 1 inhibition by SBE13. Cell Cycle 10, 708-720.
• Hartenfeller, M., Eberle, M., Meier, P., Nieto-Oberhuber, C., Altmann, K. H., Schneider, G., Jacoby, E. and Renner, S. (2011) A collection of robust organic synthesis reactions for in silico molecule design. J. Chem. Inf. Model. 51, 3093-3098.
• Horvath, D., Koch, C., Schneider, G., Marcou, G. and Varnek, A. (2011) Local neighborhood behavior in a combinatorial library context. J. Comput. Aided Mol. Des. 25, 237-252.
• Hieke, M., Greiner, C., Dittrich, M., Reisen, F., Schneider, G., Schubert-Zsilavecz, M. and Werz, O. (2011) Discovery and biological evaluation of a novel class of dual microsomal prostaglandin E2 synthase 1/5-lipoxygenase inhibitors based on (2-[4,6-diphenethoxypyrimidin-2-yl)thio]hexanoic acid. J. Med. Chem. 54, 4490-4507.
• Hüsch, J., Dutagaci, B., Glaubitz, C., Geppert, T., Schneider, G., Harms, M., Müller-Goymann, C.C., Fink, L., Schmidt, M.U., Setzer, C., Zirkel, J., Rebmann, H., Schubert-Zsilavecz, M. and Abdel-Tawab, M. (2011) Structural properties of the so-called NSAID-phospholipid-complexes. Eur. J. Pharm. Sci. 44, 103-116.
• Knauer, S. K., Fetz, V., Rabenstein, J., Friedl, S., Hofmann, B., Sabiani, S., Schröder, E., Kunst, L., Proschak, E., Thines, E., Kindler, T., Schneider, G., Marschalek, R. and Stauber, R. H. (2011) Bioassays to monitor Taspase 1 function for the identification of pharmacogenetic inhibitors. PLoS ONE 6, e18253.
• Rödl, C. B., Tanrikulu, Y., Wisniewska, J. M., Proschak, E., Schneider, G., Steinhilber, D. and Hofmann, B. (2011) Potent inhibitors of 5-lipoxygenase identified using pseudoreceptors. ChemMedChem 6, 1001-1005.
• Deng, W., Schneider, G. and So, W. V. (2011) Mapping chemical structures to Markush structures using SMIRKS. Mol. Inf. 30, 665-671.
• Schneider, G. (2011) From hits to leads: Challenges for the next phase of machine learning in medicinal chemistry. Mol. Inf. 30, 759-763.
• Bremm, M., Huenecke, S., Lehrnbecher, T., Ponstingl, E., Mueller, R., Heinze, A., Bug, G., Quaiser, A., Kapinsky, M., Brehm, C., Bader, P., Schneider, G., Klingbiel, T. and Koehl, U. (2011) Advanced flowcytometric analysis of regulatory T cells: CD127 downregulation early post stem cell transplantation and altered Treg/CD3(+)CD4(+)- ratio in patients with severe GvHD or relapse. J. Immunol. Methods 373, 36-44.
  
• Hiss, J. A. and Schneider, G. (2011) Sorting potential therapeutic targets in Apicomplexa. In: Apicomplexan Parasites (Becker, K.; ed.), Drug Discovery in Infectious Deseases Vol. 2, Wiley-VCH, Weinheim, pp. 35-51.
• Schneider, G. (2011) Lab presentation: The computer-assisted drug design group at ETH Zurich. MedChemWatch 12, 55-57.
• Schneider, G. (2011) Author profile. ChemMedChem 6, 1150-1151.

Edited volumes:

• Schneider, G. (ed.) Special focus issue, parts I-III: Computational Medicinal Chemistry. Future Med. Chem. 3:4,6,7 (2011).
• Nishiyama, T., Schneider, G. and Wrede, P. (eds) Thematic series: Advances in Peptide Chemistry and Medicinal Application. Chem. Cent. J. 5 (2011).
• Baldi, P., Müller, K. R. and Schneider, G. (eds) Special issue: Charting Chemical Space: Challenges and Opportunities for Artificial Intelligence and Machine Learning. Mol. Inf. 30:9 (2011).
  

2010

• Schneider, G. (2010) Virtual screening: An endless staircase? Nat. Rev. Drug Discov. 9, 273-276.
• Reisen, F., Weisel, M., Kriegl, J. M. and Schneider, G. (2010) Self-organizing fuzzy graphs for structure-based comparison of protein pockets. J. Proteome Res. 9, 6498-6510.
• Klenner, A., Hartenfeller, M., Schneider, P. and Schneider, G. (2010) 'Fuzziness' in pharmacophore-based virtual screening and de novo design. Drug Discov. Today Technol. 7, e237-e244.
• Werner, T., Sander, K., Tanrikulu, Y., Kottke, T., Proschak, E., Stark, H. and Schneider, G. (2010) In silico characterization of ligand binding modes in the human histamine H4 receptor and their impact on receptor activation. ChemBioChem 11, 1850-1855.
  
• Zander, J., Hartenfeller, M., Hähnke, V., Proschak, E., Besier, S., Wichelhaus, T. A. and Schneider, G. (2010) Multistep virtual screening for rapid and efficient identification of non-nucleoside bacterial thymidine kinase inhibitors. Chemistry Eur. J. 16, 9630-9637. 
• Hoy, B., Löwer, M., Weydig, C., Carra, G., Tegtmeyer, N., Geppert, T., Schröder, P., Sewald, N., Backert, S., Schneider, G. and Wessler, S. (2010) Helicobacter pylori HtrA is a new secreted virulence factor that cleaves E-Cadherin to disrupt intercellular adhesion. EMBO Rep. 11, 798-804.
• Zettl, H., Weggen, S., Schneider, P. and Schneider, G. (2010) Exploring chemical space of gamma-secretase modulators. Trends Pharm. Sci. 31, 402-410.
• Weisel, M., Kriegl, J. M. and Schneider, G. (2010) Architectural repertoire of ligand binding pockets on protein surfaces. ChemBioChem 11, 556-563.
• Hiss, J. A., Hartenfeller, M. and Schneider, G. (2010) Concepts and applications of “natural computing” techniques in de novo drug and peptide design. Curr. Pharm. Des. 16, 1656-1665.
• Tanrikulu, Y., Kandru, R., Schneider, G., So, W. V. and Bitter, H.-M. (2010) Missing value estimation for compound-target activity data. Mol. Inf. 29, 678-684.
• Wisniewska, J. M., Jäger, N., Freier, A., Losch, F. O., Wiesmüller, K. H., Walden, P., Wrede, P., Schneider, G. and Hiss, J. A. (2010) MHC I stabilizing potential of computer-designed octapeptides. J. Biomed. Biotechnol., 396847.
• Koenig, M., Huenecke, S., Salzmann, E. Esser, R. Quatitsch, R., Steinhilber, D., Radeke, H. H., Martin, H., Bader, P., Klingbiel, T., Schwabe, D., Schneider, G., Lehrnbecher, T., Orth, A. and Koehl, U. (2010) Multivariate analyses of immune reconstitution in children after allo-SCT: Risk-estimation based on age-matched leukocyte sub-populations. Bone Marrow Transpl. 45, 613-621.
  
• Alamuri, P., Löwer, M., Hiss, J. A., Himpsl, S. D., Schneider, G. and Mobley, H. L. T. (2010) Adhesion, invasion, and agglutination mediated by two trimeric autotransporters in human uropathogen Proteus mirabilis. Infect. Immun. 78, 4882-4894.
• Haehnke, V., Rupp, M., Krier, M., Rippmann, F. and Schneider, G. (2010) Pharmacophore alignment search tool (PhAST): Influence of canonical atom labeling on similarity searching. J. Comput. Chem. 31, 2810-2826.
• Stauch, B., Simon, B., Basile, T. Schneider, G., Malek, N.P., Kalesse, M. and Carlomagno, T. (2010) Structure and intermolecular interaction of a reversible cyclic peptide inhibitor of the proteasome revealed by a combination of NMR spectroscopy and molecular modeling. Angew. Chem. Int. Ed. 49, 3934-3938.
• Steri, R., Kara, M., Proschak, E., Steinhilber, D., Schneider, G. and Schubert-Zsilavecz, M. (2010) Antidiabetic sulfonylureas modulate farnesoid X receptor activation and target gene transcription. Future Med. Chem. 2, 575-586.
  
• Thieme, T. M., Steri, R., Proschak, E., Paulke, A., Schneider, G. and Schubert-Zsilavecz, M. (2010) Rational design of a subtype selective pirinixic acid derived PPARγ modulator. Bioorg. Med. Chem. Lett. 20, 2469-2473.
• Sander, K., Kottke, T., Proschak, E., Tanrikulu, Y., Schneider, E.H., Seifert, R., Schneider, G. and Stark, H. (2010) Lead identification and optimization of diaminopyrimidines as histamine H4 receptor ligands. Inflamm. Res. 59, S249-S251.
  
• Rupp, M. and Schneider, G. (2010) Graph kernels for molecular similarity. Mol. Inf. 29, 266-273.
• Leuner, K., Heiser, J., Derksen, S., Fehske, C. J., Essin, K., Gollasch, M., Schneider, G., Harteneck, C., Chatterjee, S. S. and Mueller, W. E. (2010) Several simple 2,4 diacylphloroglucinols are specific TRPC6 activators – identifying the pharmacophore of hyperforin. Mol. Pharmacol. 77, 368-377.
• Steri, R., Schneider, P., Klenner, A., Rupp, M., Schubert-Zsilavecz, M. and Schneider, G. (2010) Target profile prediction: cross-activation of peroxisome proliferator-activated receptor (PPAR) and farnesoid X receptor (FXR). Mol. Inf. 29, 287-292.
• Klenner, A., Weisel, M., Reisen, F., Proschak, E. and Schneider, G. (2010) Automated docking of complex and flexible molecules into receptor binding sites by ligand self-organization. Mol. Inf. 29, 189-193.
• Keppner, S., Proschak, E., Kaufmann, M., Stebhardt, K., Schneider, G. and Spänkuch, B. (2010) Biological implication of freezing Plk1 in its inactive conformation in cancer cells. Cell Cycle 9, 761-763.
• Geppert, T., Proschak, E. and Schneider, G. (2010) Protein-protein docking by shape-complementarity and property matching. J. Comput. Chem. 31, 1919-1928.
• Rupp, M., Schroeter, T., Steri, R., Zettl, H., Proschak, E., Hansen, K., Rau, O., Schwarz, O., Müller-Kuhrt, L., Schubert-Zsilavecz, M., Müller, K.-R. and Schneider, G. (2010) From machine learning to natural product derivatives selectively activating transcription factor PPARg. ChemMedChem, 5, 191-194.
• Roersch, F., Wobst, Y., Zettl, H., Schubert-Zsilavecz, M., Groesch, S., Geisslinger, G., Schneider, G. and Proschak, E. (2010) Non-acidic inhibitors of human microsomal prostaglandin synthase 1 (mPGES 1) identified by a multi-step virtual screening protocol. J. Med. Chem., 53, 911-915.
• Jäger, N., Wisniewskaja, J. M., Hiss, J. A., Losch, F. O., Walden, P., Wrede, P. and Schneider, G. (2010) Attractors in sequence space: agent-based exploration of MHC I binding peptides. Mol. Inf. 29, 65-74.
• Schneider, G. (2010) From virtual to real screening – Achievements and challenges for similarity searching. EFMC Yearbook 2010, pp. 33-45.
• Schmuker, M. and Schneider, G. (2010) Brain-like processing and classification of chemical data: An approach inspired by the sense of smell. In: Chemoinformatics and Advanced Machine Learning Perspectives (Lodhi, H. and Yamanishi, Y., Eds.), Hershey, New York, pp. 289-302.

see PDF for earlier publications