• Buscató, E., Proschak, E. 5-Lipoxygenase Inhibitors: A Patent Evaluation (WO2011161615) Expert Opin. Ther. Patents accepted
  
• Rörsch, F., Buscató, E., Deckmann, K., Schneider, G., Schubert-Zsilavecz, M., Geisslinger, G., Proschak, E., Grösch, S. Structure Activity Relationship of Non-acidic Quinazoline Inhibitors of Human Microsomal Prostaglandin Synthase 1 (mPGES-1) J. Med. Chem. accepted
• Steri, R., Achenbach, J., Steinhilber, D., Schubert-Zsilavecz, M., Proschak, E. Investigation of imatinib and other approved drugs as starting points for antidiabetic drug discovery with FXR modulating activity. Biochem Pharmacol. accepted.
• Moser, D., Wisniewska, J.M, Hahn, S., Buscató, E., Klingler, F.-M., Achenbach, J., Hofmann, B., Steinhilber, D., Proschak, E. Dual-target virtual screening by pharmacophore elucidation and molecular shape filtering. ACS Med. Chem. Lett. accepted
• Hieke, M., Rödl, C.B.,Wisniewska, J.M., Buscató, E., Stark, H., Schubert-Zsilavecz, M., Steinhilber, D., Hofmann, B., Proschak, E. SAR-study on a new class of imidazo[1,2-a]pyridine based inhibitors of 5-lipoxygenase. Bioorg. Med. Chem. Lett. accepted
• Hartenfeller, M., Zettl, H., Walter, M., Rupp, M., Reisen, F., Proschak, E., Weggen, S., Stark, H., Schneider, G. DOGS: Reaction-driven de novo design of bioactive compounds. PLoS Comput. Biol. accepted

• Wisniewska, J.M., Rödl, C.B., Kahnt, A.S.,Buscató, E., Ulrich, S., Tanrikulu, Y., Achenbach, J., Rörsch, F., Grösch, S., Schneider, G., Cinatl Jr., J.,  Proschak, E., Steinhilber, D., Hofmann, B. Molecular Characterization of EP6 - a Novel Direct Pyridine-imidazole Based 5-Lipoxygenase Inhibitor. Biochem. Pharmacol. accepted
• Hahn, S., Achenbach, J., Buscató, E., Klingler, F., Schroeder, M., Meirer, K., Hieke, M., Heering, J., Barbosa-Sicard, E., Löhr, F., Fleming, I., Doetsch, V., Schubert-Zsilavecz, M., Steinhilber, D., Proschak, E. Complementary screening techniques yielded fragment inhibitors of phosphatase activity of soluble epoxide hydrolase. ChemMedChem accepted
• Rödl, C., Tanrikulu, Y., Wisniewska, J.M., Proschak, E., Schneider, G., Steinhilber, D., Hofmann, B. (2011) Potent Inhibitors of 5-Lipoxygenase Identified Using Pseudoreceptors. ChemMedChem, 6, 1001-1005.
• Löwer, M., Proschak, E. (2011) Structure-based pharmacophores for virtual screening. Mol. Inf., 30, 398-404.
• Achenbach, J., Tikkainen, P., Franke, L., Proschak, E. (2011) Computational tools for polypharmacology and repurposing Future Med. Chem., 3, 961-968.
• 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., Stauber, R.H., Bier, C. (2011) Bioassays to monitor Taspase1 function for the identification of pharmacogenetic inhibitors. PLoS One, 6, e18253.
• Keppner, S., Proschak, E., Hahn, C., Schneider, G., 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.
• Urbanek, D., Proschak, E., Tanrikulu, Y., Becker, S., Karas, M., Schneider, G. (2011) Scaffold-hopping from aminoglycosides to small synthetic inhibitors of bacterial protein biosynthesis using a pseudoreceptor model. MedChemComm, 2, 181-184.

2010

• Werner, T., Sander, K., Tanrikulu, Y., Kottke, T., Proschak, E., Stark, H., 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., Haehnke, V., Proschak, E., Besier, S., Wichelhaus T.A., Schneider, G., (2010) Multi-step virtual screening for rapid and efficient identification of non-nocleoside bacterial thymidine kinase inhibitors, Chem. Eur. J., 16, 9630-9637
• Schneider G., Hartenfeller M., Proschak, E. (2010) “De Novo Design” in Lead Generation Approaches in Drug Discovery, Rankovic Z., Morphy R. Ed., John Wiley & Sons: Hoboken, N.J.
• Thieme, T., Steri, R., Proschak, E., Paulke, A., Schneider, G., Schubert-Zsilavecz, M. (2010) Rational design of a pirinixic acid derivative that acts as subtype-selective PPARgamma modulator, Bioorg. Med. Chem. Lett., 20, 2469-2473.
• Steri, R., Rupp, M., Proschak, E., Schroeter, T., Zettl, H., Hansen, K., Schwarz, O., Müller-Kuhrt, L., Müller, K.-R., Schneider, G., Schubert-Zsilavecz, M. (2010) Truxillic acid derivatives act as peroxisome proliferator-activated receptor gamma activators, Bioorg Med Chem Lett., 20, 2920-2923.
• Sander, K., Kottke, T., Proschak, E., Tanrikulu, Y., Schneider, E.H., Seifert, E., Schneider, G., Stark, H. (2010) Lead identification and optimization of diaminopyrimidines as histamine H(4) receptor ligands. Inflamm. Research, 59, S249-S251.
• 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., Schneider, G. (2010) From machine learning to natural product derivatives selectively activating transcription factor PPARgamma. ChemMedChem, 5, 191-194.
• Steri, S., Kara, M., Proschak, E., Steinhilber, D., Schneider, G., Schubert-Zsilavecz, M. (2010) Antidiabetic sulfonylureas modulate farnesoid X receptor activation and target gene transcription. Future Med Chem., 2, 575-586.
• Keppner, S., Proschak, E., Strephardt, K., Schneider, G., Spänkuch, B. (2010) Biological impact of freezing Plk1 in its inactive conformation in cancer cells. Cell Cycle, 9, 761-774.
• Geppert, T., Proschak, E., Schneider, G. (2010) Protein-Protein Docking by Shape-Complementarity and Property Matching. J. Comp. Chem., 31, 1919-1928.
• Rörsch, F., Wobst, I., Zettl, H., Schubert-Zsilavecz, M., Grösch, S., Geisslinger, G., Schneider G., 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.
• Sander, K., Kottke, T., Tanrikulu, Y., Proschak, E., Weizel, L., Schneider, E.H., Seifert, E., Schneider, G., Stark, H. (2009) 2,4-Diaminopyrimidines as Histamine H4 Receptor Ligands Scaffold Optimization and Pharmacological Characterization. Bioorg. Med. Chem., 17, 7186-7196
• Klenner, A., Weisel, M., Reisen, F., Proschak, E., Schneider, G. (2010) Automated Docking of Complex and Flexible Molecules Into Receptor Binding Sites by Ligand Self-Organization. Mol. Inf., 29, 189-193.

2009

• Keppner, S., Proschak, E., Schneider, G., Spänkuch, B. (2009) Identification and Validation of a Potent Type II Inhibitor of Inactive Polo-like Kinase 1. ChemMedChem, 4, 1806-1809.
• Zettl, H., Dittrich, M., Steri, R., Proschak, E., Rau, O., Steinhilber, D., Schneider, G., Lämmerhofer, M., Schubert-Zsilavecz, M. (2009) Novel Pirinixic Acids as PPARa Preferential Dual PPARalpha/gamma Agonists. QSAR Comb. Sci., 28, 576-586.
• Tanrikulu, Y., Proschak, E., Werner, T., Geppert, T., Todorov, N., Klenner, A., Kottke, T., Sander, K., Schneider, E., Seifert, R., Stark, H., Clark, T., Schneider, G. (2009) Homology-model adjustment and ligand screening with a pseudoreceptor of human histamine H4 receptor. ChemMedChem, 4, 820-827.
• Proschak, E., Sander, K., Zettl, H., Tanrikulu, Y., Rau, O., Schneider, P., Schubert-Zsilavecz, M., Stark, H., Schneider, G. (2009) From molecular shape to potent bioactive agents II: Fragment-based de novo design. ChemMedChem, 4, 45-48.
• Proschak, E., Zettl, H., Tanrikulu, Y., Weisel, M., Kriegl, J.M., Rau, O., Schubert-Zsilavecz, M., Schneider, G. (2009) From molecular shape to potent bioactive agents I: Bioisosteric replacement of molecular fragments. ChemMedChem, 4, 41-44.
• Reisen, F., Schneider, G., Proschak, E. (2009) Reaction-MQL: line notation for representation of chemical reactions. J. Chem. Inf. Model., 49, 6-12.
• Schneider, G., Hartenfeller, M., Reutlinger, M., Tanrikulu, Y., Proschak, E., Schneider, P. (2009) Voyages to the (un)known: Adaptive design of druglike compounds. Trends in Biotech., 27, 18-26.
• Tanrikulu, Y., Rau, O., Schwarz, O., Proschak, E., Siems, K., Müller-Kuhrt, L., Schubert-Zsilavecz, M., Schneider, G., (2009) Structure-based Pharmacophore Screening for Natural Product-derived PPARgamma Agonists. ChemBioChem, 10, 75-78.
• Weisel, M., Proschak, E., Kriegl, J., Schneider G. (2009) Form Follows Function:Shape Analysis of Protein Cavities for Receptor-based Drug Design. Proteomics, 9, 451-459.
• Hähnke, V., Hofmann, B., Grgat, T., Proschak, E., Steinhilber, D., Schneider, G., (2009) PhAST: Pharmacophore Alignment Search Tool. J. Comput. Chem., 30, 761-771.

2008

• Hofmann, B., Franke, L., Proschak, E., Tanrikulu, Y., Schneider, P., Steinhilber, D., Schneider, G.(2008) Scaffold-hopping cascade yields potent inhibitors of 5-lipoxygenase. ChemMedChem, 3, 1535-1538.
• Grabowski, K., Proschak, E., Baringhaus, K.-H., Rau, O., Schubert-Zsilavecz, M., Schneider, G. (2008) Bioisosteric Replacement of Molecular Scaffolds: From Natural Products to Synthetic Compounds. Nat. Prod. Comm., 3, 1355-1360.
• Hartenfeller, M., Proschak, E., Schüller, A., Schneider, G. (2008) Concept of Combinatorial De Novo Design of Drug-like Molecules by Particle Swarm Optimization. Chem Biol. Drug Des. 72, 16-26.
• Proschak, E., Tanrikulu, Y. and Schneider, G. (2008) Fragment-based de novo design of druglike compound libraries. In: Chemoinformatics: An Approach to Virtual Screening (A.Varnek, A. Tropsha; Eds). RSC Publishing, Cambridge, 217-239.

2007

• Rupp, M., Proschak, E., Schneider, G. (2007) Kernel approach to molecular similarity based on iterative graph similarity. J. Chem. Inf. Model. 47, 2280-2286.
• Tanrikulu, Y., Nietert, M., Scheffer, U., Proschak, E., Grabowski, K., Schneider, P., Weidlich, M., Karas, M., Göbel, M., Schneider, G.(2007) Scaffold Hopping by "Fuzzy" Pharmacophores and its Application to RNA Targets. ChemBioChem, 8, 1232-1236
• Proschak, E., Rupp, M., Derksen, S. and Schneider, G. (2007) Shapelets: possibilities and limitations of shape-based virtual screening. J. Comp. Chem. 29, 108-114.
• Schneider, G., Proschak, E., Grabowski, K., Schneider, P. and Tanrikulu, Y. (2007) More than colored blobs – “Fuzzy” descriptions of potential pharmacophore points. In: Proceedings of the Beilstein Workshop 2006 (M. Hicks, C. Kettner, Eds), Logos-Verlag, Berlin.
• Schmuker, M., Schwarte, F., Brück, A., Proschak, E., Tanrikulu, Y., Givehchi, A., Scheiffele, K. and Schneider, G. (2007) SOMMER: Self-organizing maps for education and research. J. Mol. Model., 13, 225-228.
• Weisel, M., Proschak, E. and Schneider, G. (2007) PocketPicker: Analysis of ligand binding sites with shape descriptors. Chem. Cent. J., 1, 7.
• Proschak, E., Wegner, J., Schüller, A., Schneider, G., Fechner, U. (2007) Molecular Query Language (MQL): A context-free grammar for substructure matching. J. Chem. Inf. Model., 47, 295-301.