Publications

Download1990-2009 (PDF, 151 KB)vertical_align_bottom

Books published by Prof. G. Schneider

• Atz, K., Cotos Muñoz, L., Isert, C., Håkansson, M., Focht, D., Hilleke, M., Nippa, D. F., Iff, M., Ledergerber, J., Schiebroek, C. C. G., Romeo, V., Hiss, J. A., Merk, D., Schneider, P., Kuhn, B., Grether, U. & Schneider, G. (2024) Prospective deep interactome learning for de novo drug design. external pageNat. Commun. 15, 3408call_made.
• Nippa, D. F., Atz, K., Hohler, R., Müller, A. T., Marx, A., Bartelmus, C., Wuitschik, G., Marzuoli, I., Jost, V., Wolfard, J., Binder, M., Stepan, A. F., Konrad, D. B., Grether, U., Martin, R. E. & Schneider, G. (2024) Enabling late-​stage drug diversification by high-​throughput experimentation with geometric deep learning. external pageNat. Chem. 16, 239–248call_made.
  
• Allenspach, S., Hiss, J. A. & Schneider, G. (2024) Neural multi-task learning in drug design. external pageNat. Mach. Intell. 6, 124-137call_made.
• Tropsha, A., Isayev, O., Varnek, A., Schneider, G. & Cherkasov, A. (2024) Integrating QSAR modelling and deep learning in drug discovery: The emergence of deep QSAR. external pageNat. Rev. Drug Discov. 23, 141-155call_made.
• Isert, C., Atz. K., Riniker, S. & Schneider, G. (2024) Exploring protein-​ligand binding affinity prediction with electron density-​based geometric deep learning. external pageRSC Advances 14, 4492-4502call_made.
• Faquetti, M. L., Slappendel, L., Bigonne, H., Aichinger, G., Grisoni, F., Schneider, P., Schneider, G., Burden, A. & Sturla, S. (2024) Baricitinib and tofacitinib off-target profile, with a focus on Alzheimer’s disease. external pageAlzheimer's Dement.10, e12445call_made.

• Moret, M., Pachon Angona, I., Cotos Muñoz, L., Yan, S., Atz, K., Brunner, C., Baumgartner, M., Grisoni, F. & Schneider, G. (2023) Leveraging molecular structure and bioactivity with chemical language models for drug design. external pageNat. Commun. 14, 114.call_made
• Ilnicka, A. & Schneider, G. (2023) Designing molecules with autoencoder networks. external pageNat. Comput. Sci. 3, 922-933call_made.
• Nippa, D. F., Atz, K., Müller, A. T., Wolfard, J., Isert, C., Binder, M., Scheidegger, O., Konrad, D. B., Grether, U., Martin, R. E. & Schneider, G. (2023) Identifying opportunities for late-stage C-H alkylation with in silico reaction screening and high-throughput experimentation. external pageCommun. Chem. 6, 256call_made.
• Isert, C., Atz. K. & Schneider, G. (2023) Structure-based drug design with geometric deep learning. external pageCurr. Opin. Struct. Biol. 79, 102548.call_made 
• Nippa, D. F. Müller, A. T., Atz, K., Konrad, D. B., Grether, U., Martin, R. E. & Schneider, G. (2023) Simple user-friendly reaction format. Preprint: external pageChemRxiv-2023-nfq-7hcall_made.
• Ilnicka, A. & Schneider, G. (2023) Compression of molecular fingerprints with autoencoder networks. external pageMol. Inf. 42, 202300059call_made.
• Isert, C., Kromann, J. C., Stiefl, N., Schneider, G. & Lewis, R. (2023) Machine learning for fast, quantum mechanics-based approximation of drug lipophilicity. external pageACS Omega 8, 2046-2056call_made.
  
• Mancuso, R. V., Schneider, G., Hürzeler, M., Gut, M., Zurflüh, J., Breitenstein, W., Bouitbir, J., Reisen, F., Atz, K., Ehrhardt, C., Duthaler, U., Gygax, D., Schmidt, A. G., Krähenbühl, S. & Weitz-Schmidt, G. (2023) Allosteric targeting resolves limitations of earlier LFA-1 directed modalities. external pageBiochem. Pharmacol. 115504call_made.
• Neeser, R., Isert C., Stuyver, T., Schneider, G. & Coley, C. W. (2023) QMugs 1.1: Quantum mechanical properties of organic compounds commonly encountered in reactivity datasets. external pageChem. Data Collect. 46, 101040call_made.

• Isert, C., Atz, K., Jiménez-Luna, J. & Schneider, G. (2022) QMugs: Quantum mechanical properties of drug-like molecules. external pageSci. Data 9, 273call_made.
  
• Moret, M., Grisoni, F. Katzberger, P. & Schneider, G. (2022) Perplexity-based molecule ranking and bias estimation of chemical language models. external pageJ. Chem. Inf. Comput. Sci. 62, 1199-1206call_made.
• Atz, K., Isert, C., Böcker, N. M. A., Jiménez-Luna, J. & Schneider, G. (2022) Δ-Quantum machine learning for medicinal chemistry. external pagePhys. Chem. Chem. Phys. 24, 10775-10783call_made.
• Schneider, P., Altmann, K.-H. & Schneider, G. (2022) Generating bioactive natural product-inspired molecules with machine intelligence. external pageChimia 76, 396-401call_made.
• Möller, L., Guerci, L., Isert, C., Atz, K. & Schneider, G. (2022) Translating from proteins to ribonucleic acids for ligand-binding site detection. external pageMol. Inf. 41, 202200059call_made.
• Atz, K., Guba, W., Grether, U. & Schneider, G. (2022) Machine learning and computational chemistry for the endocannabinoid system. external pageMethods Mol. Biol. 2576, 477-493call_made. 
• Grisoni, F. & Schneider, G. (2022) De novo molecular design with chemical language models. external pageMethods Mol. Biol. 2390, 207-232call_made.
• Faquetti, M. L., Grisoni, F., Schneider, P., Schneider, G. & Burden, A. (2022) Off-target profiling of tofacitinib and baricitinib by machine learning: A focus on thrombosis and viral infection. external pageSci. Rep. 12, 7843call_made.
• Kumar, K. S., Brunner, C., Schuster, M., Kopp, L. L., Gries, A., Yan, S., Jurt, S., Moehle, K., Bruns, D., Grotzer, M., Zerbe, O., Schneider, G. & Baumgartner, M. (2022) Discovery of a small molecule ligand of FRS2 that inhibits invasion and tumor growth. external pageCell. Oncol.call_made, in press.

• Atz, K., Grisoni, F. and Schneider, G. (2022) Geometric deep learning on molecular representations. external pageNat. Mach. Intell. 3, 1023–1032call_made.
• Grisoni, F., Huisman, B., Button, A., Moret, M., Atz, K., Merk, D. and Schneider, G. (2021) Combining generative artificial intelligence and on-chip synthesis for de novo drug design. external pageSci. Adv. 7, eabg3338call_made.
• Friedrich, L., Cingolani, G., Ko, Y.-H., Iaselli, M., Miciaccia, M., Perrone, M. G., Neukirch, K., Bobinger, V., Merk, D., Hofstetter, R. K., Werz, O., Koeberle, A., Scilimati, A. and Schneider, G. (2021) Learning from nature: From a marine natural product to synthetic cyclooxygenase-1 inhibitors by automated de novo design. external pageAdv. Sci. 8, 2100832call_made.
• Jiménez-Luna, J., Grisoni, F. Weskamp, N. and Schneider, G. (2021) Artificial intelligence in drug discovery: Recent advances and future perspectives. external pageExpert Opin. Drug Discov. 16, 949-959call_made.
• Jiménez-Luna, J., Skalic, M., Weskamp, N. and Schneider, G. (2021) Coloring molecules with explainable artificial intelligence for preclinical relevance assessment. external pageJ. Chem. Inf. Model. 61, 1083–1094call_made.
  
• Grisoni, F. and Schneider, G. (2021) De novo molecular design with chemical language models. external pageMethods Mol. Biol. 2390, 207-232call_made.
• Grisoni, F. and Schneider, G. (2021) Molecular scaffold hopping via holistic molecular representation. external pageMethods Mol. Biol. 2266, 11-35call_made.
• Moret, M., Helmstädter, M., Grisoni, F., Schneider, G. & Merk, D. (2021) Beam search sampling for molecular design and intrinsic prioritization with machine intelligence. external pageAngew. Chem. Int. Ed. 60, 19477–19482call_made.
• Aeschimann, W., Kammer, S., Staats, S., Schneider, P., Schneider, G., Rimbach, G., Cascella, M. and Stocker, A.  (2021) Engineering of a functional γ-tocopherol transfer protein. external pageRedox Biology 38, 101773call_made.
• Fino, R., Lenhart, D., Kalel, V.C., Softley, C.A., Napolitano, V., Byrne, R., Schliebs, W., Dawidowski, M., Erdmann, R., Sattler, M., Schneider, G., Plettenburg, O. and Popowicz GM. (2021) Computer-aided design and synthesis of a new class of PEX14 inhibitors: Substituted 2,3,4,5-tetrahydrobenzo[F][1,4]oxazepines as potential new trypanocidal agents. external pageJ. Chem. Inf. Model. 61, 5256-5268call_made.
  
• Kaeslin, J., Brunner, C., Ghiasikhou, S., Schneider G,. and Zenobi, R. (2021) Bioaffinity screening with a rapid and sample-efficient autosampler for native electrospray ionization mass spectrometry. external pageAnal. Chem. 93, 13342–13350call_made.
  
• Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., Isayev, O., Kozakov, D., Medina-Franco, J., Merz, K. M., Oprea, T. I., Poroikov, V., Schneider, G., Todd, M. H., Varnek, A., Winkler, D. A., Zakharov, A., Cherkasov, A. and Tropsha, A. (2021) A critical overview of computational approaches employed for COVID-19 drug discovery. external pageChem. Soc. Rev. 50, 9121–9151call_made.
• Wu, N., Olechwier, A. M., Brunner, C. Edward, P. C.,Tsai, C.-J., Tate, C. G., Schertler, G. F. X., Schneider, G., Deupi, X., Zenobi, R. and Ma, P. (2021) High-mass MALDI-MS unravels ligand-mediated G-protein coupling selectivity to GPCRs. external pageProc. Natl. Acad. Sci. USA 118, e2024146118.call_made
• Schneider, G. (2021) An insight into artificial intelligence in drug discovery: An interview with Professor Gisbert Schneider. external pageExpert Opin. Drug Discov. 16, 933-935call_made.

• Schneider, P., Walters, W. P.,  Plowright, A. T., Sieroka, N., Listgarten, J., Goodnow Jr., R. A., Fisher, J., Jansen, J. M., Duca, J. S., Rush, T. S., Zentgraf, M., Hill, J. E., Krutoholow, E., Kohler, M., Blaney, J., Funatsu, K., Luebkemann, C. and Schneider, G. (2020) Rethinking drug design in the artificial intelligence era. external pageNature Rev. Drug Discov. 19, 353–364call_made.
• Moret, M., Friedrich, L., Grisoni, F., Merk, D. and Schneider, G. (2020) Generative molecular design in low data regimes. external pageNature Mach. Intell. 2, 171-180call_made.
• Jiménez-Luna, J., Grisoni, F. and Schneider, G. (2020) Drug discovery with explainable artificial intelligence. external pageNature Mach. Intell. 2, 573-584call_made.
  
• Rich, A. S., Rudin, C., Jacoby , D. M. P., Freeman, R., Wearn, O. R., Shevlin, H., Dihal, K., ÓhÉigeartaigh, S. S., Butcher, J., Lippi,  M., Palka, P., Torroni, P., Wongvibulsin, S., Begoli, E., Schneider, G., Cave, S., Sloane, M., Moss, E., Rahwan, I., Goldberg, K., Howard, D., Floridi, l. and Stilgoe, J. (2020) AI reflections in 2019. external pageNature Mach. Intell. 2, 2-9call_made.
  
• Grisoni, F., Moret, M., Lingwood, R. and Schneider, G. (2020) Bidirectional molecule generation with recurrent neural networks. external pageJ. Chem. Inf. Model. 60, 1175-1183call_made.
• Friedrich, L., Byrne, R., Treder, A., Singh, I., Bauer, C., Gudermann, T., Mederos y Schnitzler, M., Storch, U. and Schneider, G. (2020) Shape similarity by fractal dimensionality: An application in de novo design of (-)-Englerin A mimetics. external pageChemMedChem 15, 566-570call_made.
  
• Bruns, D., Gawehn, E., Kumar, K. S., Schneider, P., Baumgartner, M. and Schneider, G. (2020) Identification of synthetic activators of cancer cell migration by hybrid deep learning. external pageChemBioChem 21, 500-507call_made.
• Schneider, P., Welin, M., Svensson, B., Walse, B. and Schneider, G. (2020) Virtual screening and design with machine intelligence applied to Pim-1 kinase inhibitors. external pageMol. Inf. 39, 2000109call_made.
• Müller, A., Posselt, G., Gabernet, G., Neuhaus, C., Bachler, S., Blatter, M., Pfeiffer, B., Hiss, J. A., Dittrich, P., Altmann, K.-H., Wessler, S. and Schneider, G. (2020) Morphing of amphipathic helices to explore the activity and selectivity of membranolytic antimicrobial peptides. external pageBiochemistry 59, 3772–3781call_made.
  
• Li, X., Brunner, C., Wu, Y., Leka, O., Schneider, G. and Kammerer, R. A. (2020) Structural insights into the interaction of botulinum neurotoxin A with its neuronal receptor SY2C. external pageToxicon 175, 36-43call_made.
• Hajduk, J., Brunner, C., Malik, S., Bangerter, J., Schneider, G., Thomann, M., Reusch, D. and Zenobi, R. (2020) Interaction analysis of glycoengineered antibodies with CD16a: A native mass spectrometry approach. external pagemAbs 12, e1736975call_made.
• Fino, R., Byrne, R., Softley, C. A., Sattler, M., Schneider, G. and Popowicz, G. M. (2020) Introducing the CSP Analyzer: A novel machine mearning-based application for automated analysis of two-dimensional NMR spectra in NMR fragment-based screening. external pageComput. Struct. Biotechnol. J. 18, 603-611call_made.
• Bernegger, S., Brunner, C., Vizovišek, M., Fonovic, M., Cuciniello, G., Giordano, F., Stanojlovic, V., Jarzab, M., Simister, P., Feller, S. M., Obermeyer, G., Posselt, G., Turk, B., Cabrele, C., Schneider, G. and Wessler, S. (2020) A novel FRET peptide assay reveals efficient Helicobacter pylori HtrA inhibition through zinc and copper binding. external pageSci. Rep. 10, 10563call_made.
  
• Gunesch, A. P., Zapatero-Belinchon, F. J., Pinkert, L., Steinmann, E., Manns, M. P., Schneider, G., Pietschmann, T., Brönstrup, M. and von Hahn, T. (2020) Filovirus antiviral activity of cationic amphiphilic drugs is associated with lipophilicity and ability to induce phospholipidosis. external pageAntimicrob. Agents Chemother. 64, e00143-e00120call_made.

• Schneider, G. (2019) Mind and machine in drug design. external pageNature Mach. Intell. 1, 128-130call_made.
  
• Button, A., Merk, D., Hiss, J. A. and Schneider, G. (2019) Automated de novo molecular design by hybrid machine intelligence and rule-driven chemical synthesis. external pageNature Mach. Intell. 1, 307-315call_made.
• Schneider, G. and Clark, D. (2019) Automated de novo design - "Are we nearly there yet?" external pageAngew. Chem. Int. Ed. 58, 10792-10803call_made.
  
• Neuhaus, C. S., Gabernet, G., Steuer, C., Root, K., Hiss, J. A., Zenobi, R. and Schneider, G. (2019) Simulated molecular evolution for anticancer peptides. external pageAngew. Chem. Int. Ed. 58, 1674-1678call_made.
• Fuchs, J. A., Brunner, C., Schineis, P., Hiss, J. A. and Schneider, G. (2019) Identification of chemokine ligands by biochemical fragmentation and simulated peptide evolution. external pageAngew. Chem. Int. Ed. 58, 7138-7142call_made.
• Grisoni, F., Merk, D., Friedrich L. and Schneider, G. (2019) Design of natural-product-inspired multi-target ligands by machine learning. external pageChemMedChem 14, 1129-1134call_made.
• Grisoni, F. and Schneider, G. (2019) De novo molecular design with generative long short-term memory. external pageChimia 73, 1006-1011call_made.
  
• Bruns, D., Merk, D., Kumar, K. S., Baumgartner, M. & Schneider, G. (2019) Synthetic activators of cell migration designed by constructive machine learning. external pageChemistryOpen 8, 1303-1308.call_made
  
• Yang, X., Wang, Y., Byrne, R., Schneider, G. and Yang, S. (2019) Concepts of artificial intelligence for computer-assisted drug discovery. external pageChem. Rev. 119, 10520-10594call_made.
  
• Gabernet, G., Gautschi, D., Müller, A. T., Neuhaus, C. S., Armbrecht, L., Dittrich, P. S., Hiss, J. A. and Schneider, G. (2019) In silico design and optimization of selective membranolytic anticancer peptides. external pageSci. Rep. 9, 11282call_made.
• Byrne, R. and Schneider, G. (2019) In silico target prediction for small molecules. external pageMethods Mol. Biol. 1888, 273-309call_made.
• Merk, D., Grisoni, F., Schaller, K., Friedrich, L. and Schneider, G. (2019) Discovery of novel molecular frameworks of farnesoid X receptor modulators by ensemble machine learning. external pageChemistryOpen 8, 7-14call_made.
• Grisoni, F., Neuhaus, C. S., Hishinuma, M., Gabernet, G., Hiss, J. A., Kotera, M. and Schneider, G. (2019) De novo design of anticancer peptides by ensemble artificial neural networks. external pageJ. Mol. Model. 25, 112call_made.
• Bauer, C. A., Schneider, G. and Göller, A. H. (2019) Gaussian process regression models for the prediction of hydrogen bond acceptor strengths. external pageMol. Inf. 38, e1800115call_made.
• Bauer, C. A., Schneider, G. and Göller, A. H. (2019) Machine learning models for hydrogen bond donor and acceptor strengths using large and diverse training data generated by first-principles interaction free energies. external pageJ. Cheminform. 11, 59call_made.
• Grisoni, F. and Schneider, G. (2019) Molecular design with long short-term memory networks. external pageJ. Comp. Aided Chem. 20, 35-42call_made.

• Schneider, G. (2018) Automating drug discovery. Nature Rev. Drug Discov. 17, 97–113.
• Schneider, G. (2018) Generative models for artificially-intelligent molecular design. external pageMol. Inf. 37, 1880131call_made.
  
• Merk, D., Friedrich, L., Grisoni, F. and Schneider, G. (2018) De novo design of bioactive small molecules by artificial intelligence. external pageMol. Inf. 37, 1700153call_made.
• Gupta, A., Müller, A. T., Huisman, B. J. H., Fuchs, J. A., Schneider, P. and Schneider, G. (2018) Generative recurrent networks for de novo drug design. external pageMol. Inf. 37, 1700111call_made.
• Müller, A. T., Hiss, J. A. and Schneider, G. (2018) Recurrent neural network model for constructive peptide design. external pageJ. Chem. Inf. Model. 58, 472–479call_made.
• Gawehn, E., Hiss, J. A., Brown, J. B. and Schneider, G. (2018) Advancing drug discovery via GPU-based deep learning. external pageExpert Opin. Drug Discov. 13, 579–582call_made.
• Merk, D., Grisoni, F., Friedrich, L. and Schneider, G. (2018) Tuning artificial intelligence on the de novo design of natural-product-inspired retinoid X receptor modulators. external pageCommunications Chemistry 1, 68call_made.
  
• Grisoni, F., Merk, D., Consonni, V., Hiss, J. A., Tagliabue, S. G., Todeschini, R. and Schneider, G. (2018) Scaffold hopping from natural products to synthetic mimetics by holistic molecular similarity. external pageCommunications Chemistry, 1, 44call_made.
  
• Merk, D., Grisoni, F., Friedrich, L., Gelzynte, E. and Schneider, G. (2018) Scaffold hopping from synthetic RXR modulators by virtual screening and de novo design. external pageMed. Chem. Commun. 9, 1289–1292call_made.
• Merk, D., Grisoni, F., Friedrich, L., Gelzynte, E. and Schneider, G. (2018) Computer-assisted discovery of retinoid X receptor modulating natural products and isofunctional mimetics. external pageJ. Med. Chem. 61, 5442–5447call_made.
• Grisoni, F., Merk, D., Byrne, R. and Schneider, G. (2018) Scaffold-hopping from synthetic drugs by holistic molecular representation. external pageSci. Rep. 8, 16469call_made.
  
• Grisoni, F., Neuhaus, C. S., Gabernet, G., Müller, A. T., Hiss, J. A. and Schneider, G. (2018) Designing anticancer peptides by constructive machine learning. external pageChemMedChem 13, 1300–1302call_made.
• Fuchs, J. A., Grisoni, F., Kossenjans, M., Hiss, J. A. and Schneider, G. (2018) Lipophilicity prediction of peptides and peptide derivatives by consensus machine learning. external pageMed. Chem. Commun. 9, 1538-1546call_made.
• Schneider, P. and Schneider, G. (2018) Polypharmacological drug-target inference for chemogenomics. external pageMol. Inf. 37, 1800050call_made.
  
• Finkelmann, A. R., Goldmann, D., Schneider, G. and Göller, A. H. (2018) MetScore: Site of metabolism prediction beyond cytochrome P450 enzymes. external pageChemMedChem 13, 2281-2289call_made.
• Brand, S., Roy, S., Schröder, P., Rathmer, B., Roos, J., Kapoor, S., Patil, S., Pommerenke, C., Maier, T., Janning, P., Eberth, S., Steinhilber, S., Schade, D., Schneider, G., Kumar, K., Ziegler, S. and Waldmann. H. (2018) Combined proteomic and in silico target identification reveal a new role for 5-lipoxygenase in developmental signaling pathways. external pageCell Chem. Biol. 25, 1095-1106call_made.
• Gulbakan, B., Barylyuk, K., Schneider, P., Pillong, M., Schneider, G. and Zenobi, R. (2018) Native electrospray ionization mass spectrometry reveals multiple facets of aptamer-ligand interactions: from mechanism to binding constants. external pageJ. Am. Chem. Soc., 140, 7486-7497call_made.
  
• M. Köhler, C. Neff, C. Perez, C. Brunner, E. Pardon, J. Steyaert, G. Schneider, K. P. Locher and R. Zenobi (2018) Binding specificities of nanobody-membrane protein complexes obtained from chemical cross-linking and high-mass MALDI mass spectromerty. external pageAnal. Chem. 90, 5306–5313call_made.
• Allenspach, M. D., Fuchs, J. A., Doriot, N., Hiss, J. A., Schneider, G. and Steuer, C. (2018) Quantification of hydrolyzed peptides and proteins by amino acid fluorescence. external pageJ. Pept. Sci. 24, e3113call_made.
  
• Baumann, K. and Schneider, G. (2018) Cheminformatics and the mean. external pageMol. Inf. 37, 1880132call_made.
  
• Schneider, G. (2018) external pageFuture perspectives of computational drug designcall_made. In: Applied Chemoinformatics: Achievements and Future Opportunities (Engel, T., Gasteiger, J.; eds), Wiley-VCH, Weinheim, New York, pp 403-414.

Edited volume:

Schneider, G. (ed) Special Issue: Generative Models in Drug Discovery. external pageMol. Inf. 37:1call_made (2018).

• Schneider, P. and Schneider, G. (2017) A computational method for unveiling the target promiscuity of pharmacologically active compounds in silico. external pageAngew. Chem. Int. Ed. 56, 11520–11524call_made.
  
• Schneider, P. and Schneider, G. (2017) Privileged structures revisited. external pageAngew. Chem. Int. Ed. 56, 7971–7974call_made.
• Stutz, K., Müller, A. T., Hiss, J. A., Schneider, P., Blatter, M., Pfeiffer, B., Posselt, G., Kanfer, G., Kornmann, B., Wrede, P., Altmann, K.-H., Wessler, S. and Schneider, G. (2017) Peptide-membrane interaction between targeting and lysis. external pageACS Chem. Biol. 15, 2245–2249call_made.
• Pillong, M., Hiss, J. A., Schneider, P., Lin, Y.-C., Posselt, G., Pfeiffer, B., Blatter, M., Müller, A. T., Bachler, S., Neuhaus, C., Dittrich, P., Altmann, K.-H., Wessler, S. and Schneider, G. (2017) Rational design of membrane-pore-forming peptides. external pageSmall 13, 1701316call_made.
• Müller, A. T., Gabernet, G., Hiss, J. A. and Schneider, G. (2017) modlAMP: Python for antimicrobial peptides. external pageBioinformatics 33, 2753–2755call_made.
  
• Finkelmann, A. R., Göller, A. H. and Schneider, G. (2017) Site of metabolism prediction based on ab initio derived atom representations. external pageChemMedChem 12, 606–612call_made.
• Schneider, G. and Schneider, P. (2017) Macromolecular target prediction by self-organizing feature maps. external pageExpert Opin. Drug Discov. 12, 271–277call_made.
• Schneider, P. and Schneider, G. (2017) De-orphaning the marine natural product (±)-marinopyrrole A by computational target prediction and biochemical validation. external pageChem. Commun. 53, 2272–2274call_made.
• Grisoni, F., Reker, D., Schneider, P., Friedrich, L., Consonni, V., Todeschini, R., Koeberle, A., Werz, O. and Schneider, G. (2017) Matrix-based molecular descriptors for prospective virtual compound screening. external pageMol. Inf. 36, 1600091call_made.
• Schneider, P., Müller, A. T., Gabernet, G., Button, A. L., Posselt, G., Wessler, S., Hiss, J. A. and Schneider, G. (2017) Hybrid network model for "deep learning" of chemical data: Application to antimicrobial peptides. external pageMol. Inf. 36, 1600011call_made.
• Button, A. L., Hiss, J. A., Schneider, P. and Schneider, G. (2017) Scoring of de novo designed chemical entities by macromolecular target prediction. external pageMol. Inf. 36, 1600110call_made.
• Kremer, L., Baumann, M., Habenberger, P., Choidas, A., Klebl, B., Ziegler, S., Schneider, G. & Waldmann, H. (2017) Discovery of a novel Hedgehog signaling pathway inhibitor by cell-based compound discovery and target prediction. external pageAngew. Chem. Int. Ed. 56, 13021–13025call_made.
  
• Armbrecht, L., Gabernet, G., Kurth, F., Hiss, J. A., Schneider, G. and Dittrich, P. S. (2017) Characterisation of anticancer peptides at the single-cell level. external pageLab Chip 17, 2933–2940call_made.
  
• Reker, D., Schneider, P., Schneider, G. and Brown, J. B. (2017) Active learning for computational chemogenomics. external pageFuture Med. Chem. 9, 381–402call_made.
• Cui, J., Hollmén, M., Li, L., Chen, Y., Proulx, S., Reker, D., Schneider, G. and Detmar, M. (2017) New use of an old drug: Inhibition of breast cancer stem cells by benztropine mesylate. external pageOncotarget 8, 1007–1022call_made.
• Bertleff-Zieschang, N., Bechold, J., Grimm, C., Reutlinger, M., Schneider, P., Schneider, G. and Seibel, J. (2017) Exploring the structural space of the galectin-1-ligand interaction. external pageChemBioChem 18, 1477–1481call_made.
  
• Wessler, S., Schneider, G. and Backert, S. (2017) Bacterial serine protease HtrA as a promising new target for antimicrobial therapy? external pageCell Commun. Signal. 15, 4call_made.

Edited volume:

Schneider, G., Funatsu, K., Okuno, J. and Winkler, D. (eds) Special Issue: De Novo Drug Design. external pageMol. Inf. 36:1,1681031call_made (2017).

• Rodrigues, T., Reker, D., Schneider, P. and Schneider, G. (2016) Counting on natural products for drug design. external pageNature Chem. 8, 531–542call_made.
• Friedrich, L., Rodrigues, T., C. S. Neuhaus, Schneider, P. and Schneider, G. (2016) From complex natural products to simple synthetic mimetics by computational de novo design. external pageAngew. Chem. Int. Ed. 55, 6789–6792call_made.
• Schneider, G., Reker, D., Chen, T., Schneider, P. and Altmann, K.-H. (2016) De-orphaning the macromolecular targets of the natural anticancer compound doliculide. external pageAngew. Chem. Int. Ed. 55, 12408–12411call_made.
• Schneider, P. and Schneider, G. (2016) De novo design at the edge of chaos. external pageJ. Med. Chem. 59, 4077–4086call_made.
• Schneider, P., Röthlisberger, M., Reker, D. and Schneider, G. (2016) Spotting and designing promiscuous ligands for drug discovery. external pageChem. Commun. 52, 1135–1138call_made.
• Finkelmann, A. R., Göller, A. H. and Schneider, G. (2016) Robust molecular representations for modelling and design derived from atomic partial charges. external pageChem. Commun. 52, 681–684call_made.
• Reker, D., Schneider, P. and Schneider, G. (2016) Multi-objective active machine learning rapidly improves structure-activity models and reveals new protein-protein interaction inhibitors. external pageChem. Sci. 7, 3919–3927call_made.
• Gawehn, E., Hiss, J. A. and Schneider, G. (2016) Deep learning in drug discovery. external pageMol. Inf., 35, 3–14call_made.
• Gabernet, G., Müller, A. T., Hiss, J. A. and Schneider, G. (2016) Membranolytic anticancer compounds. external pageMed. Chem. Commun. 7, 2232–2245call_made.
  
• Müller, A. T., Kaymaz, A. C., Gabernet, G., Posselt, G., Wessler, S., Hiss, J. A. and Schneider, G. (2016) Sparse neural network models of antimicrobial peptide-activity relationships. external pageMol. Inf. 35, 606–614call_made.
  
• Bieler, M., Reutlinger, M., Rodrigues, T., Schneider, P., Kriegl, J. M. and Schneider, G. (2016) Designing multi-target compound libraries with Gaussian process models. external pageMol. Inf. 35, 192–198call_made.
• Schmidt, T. P., Perna, A. M., Fugmann, T., Böhm, M., Hiss, J. A., Haller, S., Götz, C., Tegtmeyer, N., Hoy, B., Rau, T. T., Neri, D., Backert, S., Schneider, G. and Wessler, S. (2016) Identification of E-cadherin signature motifs functioning as cleavage sites for Helicobacter pylori. external pageSci. Rep. 6, 23264call_made.
  
• Tegtmeyer, N., Moodley, Y., Yamaoka, Y., Ramona Pernitzsch, S., Schmidt, V., Rivas Traverso, F., Schmidt, T. P., Rad, R., Guan Yeoh, K., Bow, H., Torres, J., Gerhard, M., Schneider, G., Wessler, S. and Backert, S. (2016) Characterization of worldwide Helicobacter pylori strains reveals genetic conservation and essentiality of serine protease HtrA. external pageMol. Microbiol. 99, 925–944call_made.
• Schmidt, T. P., Götz, C., Huemer, M., Schneider, G. and Wessler, S. (2016) Clacium binding protects E-cadherin from cleavage by Helicobacter pylori HtrA. external pageGut Pathogens 8, 29call_made.
• Lüthi, H. P., Heinen, S., Schneider, G., Glöss, A., Brändle, M. P., King, R. A., Pyzer-Knapp, E., Alharbi, F. H. and Kais, S. (2015) The quantum chemical search for novel materials and the issue of data processing: The InfoMol Project. external pageJ. Comput. Chem. 15, 65–73call_made.
• Schneider, G. and Schneider, P. (2016) external pageCoping with complexity in ligand-based de novo designcall_made. In: Frontiers in Molecular Design and Chemical Information Science (Bajorath, J.; ed.), ACS Publications, pp. 143–158.

• Kirchmair, J., Göller, A. H., Lang, D., Kunze, J., Testa, B., Wilson, I. D., Glen, R. D. and Schneider, G. (2015) Predicting drug metabolism: Experiment and/or computation? external pageNature Rev. Drug Discov. 14, 387–404call_made.
  
• Reker, D. and Schneider, G. (2015) Active learning strategies in computer-assisted drug discovery. external pageDrug Discovery Today 20, 458–465call_made.
• Rodrigues, T., Reker, D., Welin, M., Caldera, M., Brunner, C., Gabernet, G., Schneider, P., Walse, B. and Schneider, G. (2015) De novo fragment design for drug discovery and chemical biology. external pageAngew. Chem. Int. Ed. 54, 15079–15083call_made.
  
• Rodrigues, T., Reker, D., Kunze, J., Schneider, P. and Schneider, G. (2015) Revealing the macromolecular targets of fragment-like natural products. external pageAngew. Chem. Int. Ed. 54, 10662–10666call_made.
• Lin, Y.-C., Lim, Y. F., Russo, E., Schneider, P., Bolliger, L., Edenharter, A., Altmann, K.-H., Halin, C., Hiss, J. A. and Schneider, G. (2015) Multidimensional design of anticancer peptides. external pageAngew. Chem. Int. Ed. 54, 10370–10374call_made.
• Rodrigues, T., Hauser, N., Reker, D., Reutlinger, M., Wunderlin, T., Hamon, J., Koch, G. and Schneider, G. (2015) Multidimensional de novo design reveals 5-HT2B receptor-selective ligands. external pageAngew. Chem. Int. Ed. 54, 1551–1555call_made.
• Perna, A. M., Rodrigues, T., Schmidt, T. P., Böhm, M., Stutz, K., Reker, D., Pfeiffer, B., Altmann, K.-H., Backert, S., Wessler, S. and Schneider, G. (2015) Fragment-based de novo design reveals a small molecule inhibitor of Helicobacter pylori HtrA. external pageAngew. Chem. Int. Ed. 54, 10244–10248call_made.
• Rodrigues, T., Lin, Y.-C., Hartenfeller, M., Renner, S., Lim, Y. F. and Schneider, G. (2015) Repurposing de novo designed entities reveals phosphodiesterase 3B and cathepsin L modulators. external pageChem. Commun. 51, 7478–7481call_made.
• Miyao, T., Reker, D., Schneider, P., Funatsu, K. and Schneider, G. (2015) Chemography of natural product space. external pagePlanta Med. 81, 429–435call_made.
• Hiss, J. A., Stutz, K., Posselt, G., Wessler, S. and Schneider, G. (2015) Attractors in sequence space: Peptide morphing by directed simulated evolution. external pageMol. Inf. 34, 709–714call_made.
• Kumar, K. S., Pillong, M., Kunze, J., Burghardt, I., Weller, M., Grotzer, M., Schneider, G. and Baumgartner, M. (2015) Computer-assisted quantification of motile and invasive capabilities of cancer cells. external pageSci. Rep. 5, 15338call_made.
• Thelemann, J., Illarinov, B., Barylyuk, K., Geist, J., Kirchmair, J., Schneider, P., Anthore, L., Root, K., Trapp, N., Bacher, A., Witschel, M., Zenobi, R., Fischer, M., Schneider, G. and Diederich, F. (2015) Aryl bis-sulfonamide inhibitors for IspF from Arabidopsis thaliana and Plasmodium falciparum. external pageChemMedChem 10, 2090–2098call_made.
  
• Lanig, H., Reisen, F., Whitley, D., Schneider, G., Banting, L. and Clark, T. (2015) In silico adoption of an orphan nuclear receptor NR4A1. external pagePLoS ONE 10, e0135246call_made.
• Henkel, A., Tausch, L., Pillong, M., Jauch, J., Karas, M., Schneider, G. and Werz, O. (2015) Boswellic acids target the human immune system-modulating antimicrobial peptide LL-37. external pagePharmacol. Res. 102, 53–60call_made.
  
• Flesch, D., Gabler, M., Lill, A., Carrasco Gomez, R., Steri, R., Schneider, G., Stark, H., Schubert-Zsilavecz, M. and Merk, D. (2015) Fragmentation of GW4064 led to a highly potent farnesoid X receptor agonist with improved drug-like properties. external pageBiooorg. Med. Chem. 23, 3490–3498call_made.
  
• Sabiani, S., Geppert, T., Engelbrecht, C., Kowarz, E., Schneider, G. and Marschalek, R. (2015) Unraveling the activation mechanism of Taspase1 which controls the oncogenic AF4-MLL fusion protein. external pageEBioMedicine 5, 386–395call_made.
• Schneider, G. and Schneider, P. (2015) Inferring associations between macromolecular drug targets by self-organizing pharmacophore fingerprints. external pageCICSJ Bulletin 33, 2–5call_made.
• Rodrigues, T. and Schneider, G. (2015) external pageIn silico screening: Hit finding from database miningcall_made. In: The Practice of Medicinal Chemistry (Wermuth, C.G., Aldous, D., Raboisson, P., Rognan, D.; eds) Academic Press, Burlington MA, pp 141–162.

• Reker, D., Perna, A. M., Rodrigues, T., Schneider, P., Reutlinger, M., Mönch, B., Koeberle, A., Lamers, C., Gabler, M., Steinmetz, H., Müller, R., Schubert-Zsilavecz, M., Werz, O. and Schneider, G. (2014) Revealing the macromolecular targets of complex natural products. external pageNature Chem. 6, 1072–1078.call_made
  
• Reker, D., Rodrigues, T., Schneider, P. and Schneider, G. (2014) Identifying the macromolecular targets of de novo designed chemical entities through self-organizing map consensus. external pageProc. Natl. Acad. Sci. USA 111, 4067–4072call_made.
• Reutlinger, M., Rodrigues, T., Schneider, P. and Schneider, G. (2014) Multi-objective molecular de novo design by adaptive fragment prioritization. external pageAngew. Chem. Int. Ed. 53, 4244–4248call_made.
• Reutlinger, M., Rodrigues, T., Schneider, P. and Schneider, G. (2014) Combining on-chip synthesis of a focused combinatorial library with in silico target prediction reveals imidazopyridine GPCR ligands. external pageAngew. Chem. Int. Ed. 53, 582–585call_made.
• Rodrigues, T., Schneider, P. and Schneider, G. (2014) Accessing new chemical entities through microfluidic technology. external pageAngew. Chem. Int. Ed. 53, 5750–5758call_made.
• Reker, D., Seet, M., Pillong, M., Kock, C. P., Schneider, P., Witschel, M. C., Rottmann, M., Freymond, C., Brun, R., Schweizer, B., Illarionov, B., Bacher, A., Fischer, M., Diederich, F. and Schneider, G. (2014) Deorphaning pyrrolopyrazines as potent multi-target antimalarial agents. external pageAngew. Chem. Int. Ed., 53, 7079–7084call_made.
• Perna, A. M., Reisen, F., Schmidt, T., Geppert, T., Pillong, M., Weisel, M., Hoy, B., Simister, P. C., Feller, S., Wessler, S. and Schneider, G. (2014) Inhibiting Helicobacter pylori HtrA protease by addressing a computationally predicted allosteric ligand binding site. external pageChem. Sci. 5, 3583–3583call_made.
• Kunze, J., Todoroff, N., Schneider, P., Rodrigues, T., Geppert, T., Reisen, F., Schreuder, H., Saas, J., Hessler, G., Baringhaus, K.-H. and Schneider, G. (2014) Targeting dynamic pockets of HIV-1 protease by structure-based computational screening for allosteric inhibitors. external pageJ. Chem. Inf. Model. 54, 987–991.call_made
• Rupp, M., Bauer, M. R., Wilcken, R., Lange, A., Reutlinger, M., Boeckler, F. M. and Schneider, G. (2014) Machine learning estimates of natural product conformational energies. external pagePLoS Comput. Biol. 10,e1003400call_made.
  
• Todoroff, N., Kunze, J., Schreuder, H., Hessler, G., Baringhaus, K.-H. and Schneider, G. (2014) Fractal dimensions of macromolecular structures. external pageMol. Inf. 33, 588–596call_made.
• Lin, Y.-C., Hiss, J. A., Schneider, P., Thelesklaf, P., Lim, Y. F., Pillong, M., Koehler, F. M., Dittrich, P., Halin, C., Wessler, S. and Schneider, G. (2014) Piloting the membrane-lytic activities of peptides by a self-organizing map. external pageChemBioChem 15, 2225–2231call_made.
  
• Rupp, M., Bauer, M. R., Wilcken, R., Lange, A., Reutlinger, M., Boeckler, F. M. and Schneider, G. (2014) Machine learning estimates of natural product conformational energies. external pagePLoS Comput. Biol. 10, e1003400.call_made
• Hiss, J. A., Reutlinger, M., Koch, C. P., Perna, A. M., Schneider, P., Rodrigues, T., Haller, S., Folkers, G., Weber, L., Baleeiro, R. B., Walden, P., Wrede, P. and Schneider, G. (2014) Combinatorial chemistry by ant colony optimization. external pageFuture Med. Chem. 6, 267–280call_made.
• Rodrigues, T. and Schneider, G. (2014) Flashback forward: Reaction-driven de novo design of bioactive compounds. external pageSynlett 25, 170–178call_made.
• Persch, E., Bryson, S., Todoroff, N. K., Eberle, C., Thelemann, J., Dirdjaja, N., Kaiser, M., Weber, M., Derbani, H., Brun, R., Schneider, G., Pai, E. F., Krauth-Siegel, R. L. and Diederich, F. (2014) Binding to large enzyme pockets: Small-molecule inhibitors of trypanothione reductase. external pageChemMedChem 9, 1880–1891call_made.
• Merk, D., Gabler, M., Carrasco-Gomez, R., Flesch, D., Hanke, T., Kaiser, A., Lamers, C., Werz, O., Schneider, G. and Schubert-Zsilavecz, M. (2014) Anthranilic acid derivatives as partial farnesoid X receptor agonists. external pageBioorg. Med. Chem. 22, 2447–2460call_made.
• Hanke, T., Lamers, C., Carrasco Gomez, R., Schneider, G., Werz, O. and Schubert-Zslilavecz, M. (2014) Identification of pirinixic acid derivatives veraing a 2-aminothiazole moiety combines dual PPARα/γ activation and dual 5-LO/mPGES-1 inhibition. external pageBioorg. Med. Chem. Lett. 24, 3757–3763call_made.
• Merk, D., Lamers, C., Ahmad, K., Carrasco-Gomez, R., Schneider, G., Steinhilber, D. and Schubert-Zsilavecz, M. (2014) Extending the structure-activity relationship of anthranilic acid derivatives as farnesoid X receptor modulators - Development of a highly potent partial farnesoid X receptor agonist. external pageJ. Med. Chem. 57, 8035–8055call_made.
• Carrasco-Gomez, R., Keppner, S., Hieke, M., Lange, L., Schneider, G., Schubert-Zsilavecz, M., Proschak, E. and Spänkuch, B. (2014) Vanillin-derived antiproliferative compounds influence Plk1 activity. external pageBioorg. Med. Chem. Lett. 24, 5063–5069call_made.
• Schneider, G., Reker, D., Rodrigues, T. and Schneider, P. (2014) Coping with polypharmacology by computational medicinal chemistry. external pageChimia 68, 648–653call_made.
  
• Schneider, G. (2014) Future de novo drug design. external pageMol. Inf. 33, 397–402.call_made
  
• Schneider, G. (2014) Breaking the data barrier in computational medicinal chemistry. external pageFuture Med. Chem. 6, 1–2.call_made
• Schneider, G. (2014) Medicines of the future. external pageSci. Technol. 2, 146–147.call_made
• Reisen, F. and Schneider, G. (2014) Computational analysis of ligand binding pockets. In: Computational Chemogenomics (S. Chong, E. Jacoby, eds), Pan Stanford Publishing, Singapore, pp. 141–170.
• Koch, C. P., Reutlinger, M., Todoroff, N., Schneider, P. and Schneider, G. (2014) external pageCATS for scaffold-hopping in medicinal chemistrycall_made. In: Scaffold-Hopping in Medicinal Chemistry (N. Brown, ed.), Wiley-VCH, Weinheim, pp. 119–130.

Edited volume:

Schneider, G. (ed.) Special focus issue, Computational Medicinal Chemistry. Future Med. Chem. 6:3 (2014).

• Rodrigues, T., Kudoh, T., Roudnicky, F., Lim, Y. F., Lin, Y. C., Koch, C. P., Seno, M., Detmar, M. and Schneider, G. (2013) Steering target selectivity and potency by fragment-based de novo drug design. external pageAngew. Chem. Int. Ed. 52, 10006-10009.call_made
  
• Spänkuch, B., Keppner, S., Lange, L., Rodrigues, T., Zettl, H., Koch, C. P., Reutlinger, M., Hartenfeller, M., Schneider P. and Schneider, G. (2013) Drugs by numbers: Reaction-driven de novo design of potent and selective anticancer leads. external pageAngew. Chem. Int. Ed. 52, 4676-4681.call_made
  
• Rodrigues, T., Roudnicky, F., Koch, C. P., Kudoh, T., Reker, D., Detmar, M. and Schneider, G. (2013) De novo design and optimization of Aurora A kinase inhibitors. external pageChem. Sci. 4, 1229-1233.call_made
  
• Koch, C. P., Perna, A. M., Pillong, M., Todoroff, N. K., Wrede, P., Folkers, G., Hiss, J. A. and Schneider, G. (2013) Scrutinizing MHC-I binding peptides and their limits of variation. external pagePLoS Comput. Biol. 9, e1003088.call_made
  
• Koch, C. P., Perna, A. M., Weissmüller, S., Bauer, S., Pillong, M., Baleeiro, R. B., Reutlinger, M., Folkers, G., Walden, P., Wrede, P., Hiss, J. A., Waibler, Z. and Schneider, G. (2013) Exhaustive proteome mining for functional MHC-I ligands. external pageACS Chem. Biol. 8, 1876-1881.call_made
• Schneider, G. (2013) De novo design - hop(p)ing against hope. Drug Discov. external pageToday Technol. 10, e453-e460.call_made
  
• Reutlinger, M., Koch, C. P., Reker, D., Todoroff, N., Schneider, P., Rodrigues, T. and Schneider, G. (2013) Chemically advanced template search (CATS) for scaffold-hopping and prospective target prediction for 'orphan' molecules. external pageMol. Inf. 32, 133-138.call_made
  
• Hähnke, V., Rupp, M., Hartmann, A. K. and Schneider, G. (2013) Pharmacophore Alignment Search Tool (PhAST): Significance assessment of chemical similarity. external pageMol. Inf. 32, 625-646.call_made
  
• Koch, C. P., Pillong, M., Hiss, J. A. and Schneider, G. (2013) Computational resources for MHC ligand identification. external pageMol. Inf. 32, 326-336.call_made
  
• Rodrigues, T., Da Cruz, P., Monasterio, M. J., Bronze, M., Gut, J., Schneider, G., Mota, M., Rosenthal, P., Prudêncio, M., Gamo, F. J., Moreira, R., Ressurreicao, A. and Ana, F. (2013) Quinolin-4(1H)-imines are potent antiplasmodial drugs targeting the liver stage of malaria. external pageJ. Med. Chem. 56, 4811–4815.call_made
  
• Lötsch, J., Schneider, G., Reker, D., Parnham M. J., Schneider, P., Geisslinger, G. and Doehring, A. (2013) Common non-epigenetic drugs as epigenetic modulators. external pageTrends Mol. Med. 12, 742-752.call_made
  
• Hanke, T., Dehm, F., Liening, S., Popella, S. D., Maczewsky, J., Pillong, M., Kunze, J., Weinigel, C., Barz, D., Kaiser, A., Wurglics, M., Lämmerhofer, M., Schneider, G., Sautebin, L., Schubert-Zsilavecz, M. and Werz, O. (2013) Aminothiazole-featured pirinixic acid derivatives as dual 5-lipoxygenase and microsomal prostaglandin E2 synthase-1 inhibitors with improved potency and efficiency in vivo. external pageJ. Med. Chem. 56, 9031-9044.call_made
  
• Hanke, T., Rörsch, F., Thieme, T., Buozas N. F., Schneider, G., Geisslinger, G., Proschak, E., Grösch, S. and Schubert-Zsilavecz, M. (2013) Synthesis and pharmacological characterization of benzenesulfonamides as dual species inhibitors of human and murine mPGES-1. external pageBioorg. Med. Chem. 21, 7874-7883.call_made
• Schneider, G., Lin, Y.-C., Koch, C. P., Pillong, M., Perna, A. M., Reutlinger, M. and Hiss, J. A. (2013) Adaptive peptide design. external pageChimia 67, 859-863.call_made
  
• Schneider, G. (2013) High time to design. external pageSci. Technol. 8, 246-247.call_made
  
• Schneider, G. and Baringhaus, K.-H. (2013) De novo design: From models to molecules. In: De Novo Molecular Design (G. Schneider, ed.) Wiley-VCH, Weinheim, pp 1-56.
  
• Hiss, J. A. and Schneider, G. (2013) Peptide design by nature-inspired computing. In: De Novo Molecular Design (G. Schneider, ed.) Wiley-VCH, Weinheim, pp 441-470.
• Schneider, G. (2013) Molecula ex machina - Maschinen machen Moleküle. In: Heilen - Gesunden: Das andere Arzneibuch (E. Kut, M. Schmid, eds) Edition Collegium Helveticum Zürich, pp 131-134.

Edited volume:

Schneider, G. (ed.) De Novo Molecular Design. external pageWiley-VCH, Weinheim (2013).call_made

• Fjell, C. D., Hiss, J. A., Hancock, R. E. W. and Schneider, G. (2012) Designing antimicrobial peptides: Form follows function. external pageNature Rev. Drug Discov. 11, 37-51.call_made
  
• 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. external pageAngew. Chem. Int. Ed. 51, 258-261.call_made
  
• 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. external pagePLoS Comput. Biol. 8, e1002380.call_made
  
• Schneider, G. (2012) Designing the molecular future. external pageJ. Comput. Aided Mol. Des. 26, 115-120call_made.
  
• 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. external pageJ. Comput. Chem. 33, 573-579.call_made
  
• Schulz, M. M. P., Reisen, F., Zgraggen, S., Fischer, S., Yuen, D., Kang, G. J., Chen, L., Schneider, G. and Detmar, M. (2012) Phenotype-based high-content chemical library screening identifies statins as inhibitors of in vivo lymphangiogenesis. external pageProc. Natl. Acad. Sci. USA 109, E2665-E2674.call_made
  
• Zettl, H., Ness, J., Hähnke, V., Beher, D., Jumpertz, T., Saric, A., Baumann, K., Pietrzik, C. U., Schneider, G. and Weggen, S. (2012) Discovery of γ-secretase modulators with a novel activity profile by text-based virtual screening. external pageACS Chem. Biol. 7, 1488-1495.call_made
  
• Leimbacher, M., Zhang, Y., Mannocci, L., Stravs, M., Geppert, T., Scheuermann, J., Schneider, G. and Neri, D. (2012) Discovery of small-molecule interleukin-2 inhibitors from a DNA-encoded chemical library. external pageChemistry Eur. J. 18, 7729-7737.call_made
  
• Reutlinger, M. and Schneider, G. (2012) Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery. external pageJ. Mol. Graphics Modell. 34, 108-117.call_made
  
• Schneider, G. (2012) From theory to bench experiment by computer-assisted drug design. external pageChimia 66, 120-124.call_made
  
• 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. external pageMol. Inf. 31, 21-26.call_made
  
• Hähnke, V., Todoroff, N., Rodrigues, T. and Schneider, G. (2012) Significance estimation for sequence-based chemical similarity searching (PhAST) and application to Aurora A kinase inhibitors. external pageFuture Med. Chem. 4, 1897-1906.call_made
  
• Lieder, F., Reisen, F., Geppert, T., Sollberger, G., Beer, H. D., Auf dem Keller, U., Schäfer, M., Detmar, M., Schneider, G. and Werner, S. (2012) Identification of UV-protective activators of nuclear factor erythroid derived 2-related factor 2 (Nrf2) by combining a chemical library screen with computer-based virtual screening. external pageJ. Biol. Chem. 287, 33001-33013.call_made
  
• 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. external pageBrit. J. Pharmacol. 165, 2304-2313.call_made
  
• Wisniewska, 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. external pageBiochem. Pharmacol. 83, 228-240.call_made
  
• 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. external pageJ. Biol. Chem. 287, 10115-10120.call_made
  
• 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 prostaglandin synthase I (mPGES1). external pageJ. Med. Chem. 55, 3792-3803.call_made
  
• 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. external pageJ. Chem. Inf. Model. 52, 1167-1178call_made.
  
• Borchers, S., Bremm, M., Lehrnbecher, T., Dammann, E., Pabst, B., Wölk, B., Esser, R., Yildiz, M., Eder. M., Stadler. M., Bader, P., Martin, H., Jarisch, A., Schneider, G., Klingebiel, T., Ganser, A., Weissinger, E. M. and Koehl, U. (2012) Sequential anti-cytomegalovirus response monitoring may allow prediction of cytomegalovirus reactivation after allogenic stem cell transplantation. external pagePLoS ONE 7, e50248.call_made
  
• Pillong, M. and Schneider, G. (2012) Representing carbohydrates by pseudoreceptor models for virtual screening in drug discovery. In: Cracking the Sugar Code by Navigating the Glycospace (C. Kettner, M. Hicks, P. Seeberger, Eds), Beilstein-Institute, Frankfurt, pp. 131-145.
  
• Meanwell, N. A., Gastreich, M., Rarey, M., Devereux, M., Popelier, P. L. A., Schneider, G. and Willett, P. (2013) Perspectives from Medicinal Chemistry. In: Bioisosters in Medicinal Chemistry (N. Brown, ed.) Wiley-VCH, Weinheim, pp 217-227.
  
• Schneider, G. (2012) Angewandte Evolutionstheorie – Perspektive für den medizinischen Fortschritt. In: Charles Darwin: Die Entstehung der Arten (P. Wrede, S. Wrede, Eds), Wiley-VCH, Weinheim, pp. 505-510.

Edited volume:

Schneider, G. (ed.) Special focus issue, Computational Chemistry. Future Med. Chem. 4:15 (2012). Interview with Gisbert Schneider. external pageFuture Med. Chem. 4, 1881-1883call_made.

• 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. external pageAngew. Chem. Int. Ed. 50, 11633-11636.call_made
• Geppert, T., Hoy, B., Wessler, S. and Schneider, G. (2011) Context-based identification of protein-protein interfaces and 'hot-spot' residues. external pageChem. Biol. 18, 344-353.call_made
• Hartenfeller, M. and Schneider, G. (2011) De novo drug design. external pageMethods Mol. Biol. 672, 299-323.call_made
  
• 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. external pageFuture Med. Chem. 3, 415-424.call_made
  
• Hartenfeller, M. and Schneider, G. (2011) Enabling future drug discovery by de novo design. external pageWIREs Comp. Mol. Sci. 1, 742-759.call_made
• 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. external pageMed. Chem. Commun. 2, 181-184.call_made
  
• Bieler, M., Heilker, R., Koeppen, H. and Schneider, G. (2011) Assay related target similarity (ARTS) - Chemogenomics approach for quantitative comparison of biological targets. external pageJ. Chem. Inf. Model. 51, 1897-1905.call_made
  
• 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. external pagePLoS ONE 6, e17986.call_made
  
• Hähnke, V., Klenner, A., Rippmann, F. and Schneider, G. (2011) Pharmacophore Alignment Search Tool: Influence of the third dimension on text-based similarity searching. external pageJ. Comput. Chem. 32, 1618-1634.call_made
  
• Hähnke, V. and Schneider, G. (2011) Pharmacophore Alignment Search Tool: Influence of scoring systems on text-based similarity searching. external pageJ. Comput. Chem. 32, 1635-1647.call_made
  
• Wang, Q., Birod, K., Angioni, C., Grösch, S., Geppert, T., Schneider, P., Rupp, M. and Schneider, G. (2011) Spherical harmonics coefficients for ligand-based virtual screening of cyclooxygenase inhibitors. external pagePLoS ONE 6, e21554.call_made
• 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. external pagePharmaceuticals 4, 1236-1247.call_made
  
• 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. external pageBiol. Chem. 392, 1097-1111.call_made
  
• 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. external pageMol. Biosyst. 7, 942-951.call_made
  
• 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. external pageJ. Med. Chem. 54, 1943-1947.call_made
  
• 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. external pageCell Cycle 10, 708-720.call_made
  
• 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. external pageJ. Chem. Inf. Model. 51, 3093-3098.call_made
  
• Horvath, D., Koch, C., Schneider, G., Marcou, G. and Varnek, A. (2011) Local neighborhood behavior in a combinatorial library context.external pageJ. Comput. Aided Mol. Des. 25, 237-252.call_made
  
• 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. external pageJ. Med. Chem. 54, 4490-4507call_made.
  
• 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. external pageEur. J. Pharm. Sci. 44, 103-116.call_made
• 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.external pagePLoS ONE 6, e18253.call_made
  
• 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. external pageChemMedChem 6, 1001-1005.call_made
  
• Deng, W., Schneider, G. and So, W. V. (2011) Mapping chemical structures to Markush structures using SMIRKS. external pageMol. Inf. 30, 665-671call_made.
  
• Schneider, G. (2011) From hits to leads: Challenges for the next phase of machine learning in medicinal chemistry. external pageMol. Inf. 30, 759-763.call_made
  
• 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. external pageJ. Immunol. Methods 373, 36-44.call_made
  
• Schneider, G. (2011) Lab presentation: The computer-assisted drug design group at ETH Zurich. external pageMedChemWatch 12, 55-57.call_made
  
• Schneider, G. (2011) Author profile.external pageChemMedChem 6, 1150-1151.call_made
  
• 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.

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).

• Schneider, G. (2010) Virtual screening: An endless staircase? external pageNature Rev. Drug Discov. 9, 273-276.call_made
  
• Reisen, F., Weisel, M., Kriegl, J. M. and Schneider, G. (2010) Self-organizing fuzzy graphs for structure-based comparison of protein pockets. external pageJ. Proteome Res. 9, 6498-6510.call_made
  
• Klenner, A., Hartenfeller, M., Schneider, P. and Schneider, G. (2010) 'Fuzziness' in pharmacophore-based virtual screening and de novo design. external pageDrug Discov. Today Technol. 7, e237-e244.call_made
• 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. external pageChemBioChem 11, 1850-1855.call_made
  
• 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. external pageChemistry Eur. J. 16, 9630-9637.call_made
  
• 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. external pageEMBO Rep. 11, 798-804.call_made
  
• Zettl, H., Weggen, S., Schneider, P. and Schneider, G. (2010) Exploring chemical space of gamma-secretase modulators. external pageTrends Pharm. Sci. 31, 402-410.call_made
  
• Weisel, M., Kriegl, J. M. and Schneider, G. (2010) Architectural repertoire of ligand binding pockets on protein surfaces. external pageChemBioChem 11, 556-563.call_made
  
• Hiss, J. A., Hartenfeller, M. and Schneider, G. (2010) Concepts and applications of “natural computing” techniques in de novo drug and peptide design. external pageCurr. Pharm. Des. 16, 1656-1665.call_made
  
• Tanrikulu, Y., Kandru, R., Schneider, G., So, W. V. and Bitter, H.-M. (2010) Missing value estimation for compound-target activity data. external pageMol. Inf. 29, 678-684.call_made
  
• 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. external pageJ. Biomed. Biotechnol. 2010, 396847.call_made
  
• 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. external pageBone Marrow Transpl. 45, 613-621.call_made
  
• 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. external pageInfect. Immun. 78, 4882-4894.call_made
  
• 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. external pageJ. Comput. Chem. 31, 2810-2826.call_made
  
• Stauch, B., Simon, B., Basile, T. Schneider, G., Malek, N.P., Kalesse, M. and Carlomagno, T. (2010) Elucidation of the structure and intermolecular interactions of a reversible cyclic-peptide inhibitor of the proteasome by NMR spectroscopy and molecular modeling. external pageAngew. Chem. Int. Ed. 49, 3934-3938.call_made
  
• 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. external pageFuture Med. Chem. 2, 575-586.call_made
  
• Thieme, T. M., Steri, R., Proschak, E., Paulke, A., Schneider, G. and Schubert-Zsilavecz, M. (2010) Rational design of a pirinixic acid derivative that acts as subtype-selective PPARγ modulator. external pageBioorg. Med. Chem. Lett. 20, 2469-2473.call_made
  
• 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. external pageInflamm. Res. 59, S249-S251.call_made
  
• Rupp, M. and Schneider, G. (2010) Graph kernels for molecular similarity. external pageMol. Inf. 29, 266-273.call_made
  
• 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. external pageMol. Pharmacol. 77, 368-377.call_made
  
• 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). external pageMol. Inf. 29, 287-292.call_made
  
• Klenner, A., Weisel, M., Reisen, F., Proschak, E. and Schneider, G. (2010) Automated docking of flexible molecules into receptor binding sites by ligand self-organization. external pageMol. Inf. 29, 189-193.call_made
  
• 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. external pageCell Cycle 9, 761-763.call_made
  
• Geppert, T., Proschak, E. and Schneider, G. (2010) Protein-protein docking by shape-complementarity and property matching. external pageJ. Comput. Chem. 31, 1919-1928.call_made
  
• 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. external pageChemMedChem, 5, 191-194.call_made
  
• Roersch, F., Wobst, Y., Zettl, H., Schubert-Zsilavecz, M., Groesch, S., Geisslinger, G., Schneider, G. and Proschak, E. (2010) Nonacidic inhibitors of human microsomal prostaglandin synthase 1 (mPGES 1) identified by a multistep virtual screening protocol. external pageJ. Med. Chem., 53, 911-915.call_made
  
• 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. external pageMol. Inf. 29, 65-74.call_made
  
• 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.