Rarey, M., Wefing, S., Lengauer, T. (1996) Placement of medium-sized molecular fragments into active sites of proteins . Journal of Computer-Aided Molecular Design, 10:41--54.

Aberer, K., Barnickel, G., Böhm, H.J., Hemm, K., Hendlich, M., Klebe, G., Kramer, B., Lemmen, C., Lengauer, T., Mietzner, T., Rarey, M., Rippmann, F., Sander, C., Vriend, G. (1995) RELIWE: Berechnung und Vorhersage von Rezeptor-Ligand Wechselwirkungen . :27--52.

Aberer, K., Hemm, K., Kramer, B., Lemmen, C., Lengauer, T., Rarey, M. (1996) Strategische Suche nach neuen Algorithmen 01. GMD Spiegel, 1(01):01.

Rarey, M., Dixon, J.S. (1998) Feature Trees: A new molecular similarity measure based on tree matching . Journal of Computer-Aided Molecular Design, 12:471-490.

Kramer, B., Rarey, M., Lengauer, T. (1997) CASP-2 experiences with docking flexible ligands using FlexX . PROTEINS: Structure, Function and Genetics, Suppl 1:1(1):221--225.

Rarey, M., Kramer, B., Lengauer, T. (1999) The Particle Concept: Placing discrete water molecules during protein-ligand docking predictions . PROTEINS: Structure, Function and Genetics, 34(1):17--28.

Rarey, M., Kramer, B., Lengauer, T. (1999) Docking of hydrophobic ligands with interaction-based matching algorithms . Bioinformatics, 15:243--250.

Matter, H., Rarey, M. (1999) Design and Diversity Analysis of Compound Libraries for Lead Discovery . In Combinatorial Organic Chemistry (Jung, G., ed.), pp. 409--439

Kramer, B., Rarey, M., Lengauer, T. (1999) Evaluation of the FlexX incremental construction algorithm for protein-ligand docking . PROTEINS: Structure, Function and Genetics, 37:228--241.

Hoffmann, Daniel, Kramer, Bernd, Washio, Takumi, Steinmetzer, Torsten, Rarey, Matthias, Lengauer, Thomas (1999) Two-Stage Method for Protein-Ligand Docking . Journal of Medicinal Chemistry, 42:4422--4433.

Kramer, B., Metz, G., Rarey, M., Lengauer, T. (1999) Ligand Docking and Screening with FlexX 01. Medicinal Chemistry Research, 7/8(01):463--478.

Rarey, M., Lengauer, T. (2000) A Recursive Algorithm for Efficient Combinatorial Library Docking . Perspectives in Drug Discovery and Design, 20:63-81.

Rarey, M. (2001) Protein-Ligand Docking in Drug Design . In Bioinformatics (Lengauer, T., ed.), Vol. 1, pp. 315-360. Wiley-VCH.

Stahl, M., Rarey, M., Klebe, G. (2001) Screening of Drug Databases . In Bioinformatics (Lengauer, T., ed.), Vol. 2, pp. 137-170. Wiley-VCH.

Rarey, M., Kramer, B., Lemmen, C., Lengauer, T., Bernd, C., Hiller, C., Sonnenburg, F., Zimmermann, M. (1998) FlexX 1.9 User Guide 01. 01, 01(01):150.

Lemmen, C., Kramer, B., Lengauer, T., Rarey, M., Bernd, C., Hiller, C., Sonnenburg, F. (1998) FlexS 1.1 User Guide 01. 01, 01(01):01.

Rarey, M. (1997) FlexV 1.2 User Guide 01. 01, 01(01):01.

Springstubbe, S., Dröge, T., Rarey, M., Zimmer, R. (1999) Protein Strukturvorhersage und Molekulares Docking 01. Bioforum, 10(01):634--636.

Rarey, M., Stahl, M. (2001) Similarity Searching in Large Combinatorial Chemistry Spaces . Journal of Computer-Aided Molecular Design, 15:497-520.

Stahl, M., Rarey, M. (2001) A Detailed Analysis of Scoring Functions for Virtual Screening . Journal of Medicinal Chemistry, 44:1035-1042.

Rarey, M., Kramer, B., Lengauer, T. (1995) Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins . Proceedings of the Third International Conference on Intelligent Systems in Molecular Biology (Rawlings et al., C., ed.)

Muegge, I., Rarey, M. (2001) Small Molecule Docking and Scoring . In Reviews in Computational Chemistry (Lipkowitz, K.B., Boyd, D.B., ed.), Vol. 17, pp. 1-60. Wiley-VCH.

Rarey, M., Lengauer, T. (2000) Searching for New Drugs in Virtual Molecule Databases 01. (European Research Consortium for Informatics and Mathematics (ERCIM) News, 01(43):10--11.

Springstubbe, S., Rarey, M., Zimmer, R. (2000) Schneller Check beim Screening: Virtuelle Suche nach neuen Zielproteinen und Wirkstoffen in Moleküldatenbanken 01. Life Science Technologien, Supplement zu LaborPraxis, PROCESS und UmweltMagazin, Mai 2000(01):32--36.

Rarey, M., Lengauer, T. (1999) Auf's Gaspedal gedrückt: Beschleunigte Suche nach neuen Wirkstoffen in virtuellen Moleküldatenbanken 01. BioTec Das Fachmagazin für Biotechnologie, 10(5):45--46.

Rarey, M., Lengauer, T. (1999) Auf der Suche nach neuen Wirkstoffen in virtuellen Moleküldatenbanken 01. Der GMD-Spiegel, 29(3/4):20--23.

Lengauer, T., Rarey, M., Zimmer, R. (1999) Bioinformatik 01. Spektrum der Wissenschaft, Dossier Software, 01(2):38--43.

Claußen, H., Buning, C., Rarey, M., Lengauer, T. (2001) FlexE: Efficient Molecular Docking into Flexible Protein Structures . Journal of Molecular Biology, 308:377-395.

Claußen, H., Buning, C., Rarey, M., Lengauer, T. (2001) Molecular Docking into the Flexible Active Site of Aldose Reductase Using FlexE 01. Rational Approaches to Drug Design: Proceedings of the 13th European Symposium on Quantitative Structure-Activity Relationships (Höltje, H.-D., Sippl, W., ed.). Prous Science, Barcelona.

Hindle, S.A, Rarey, M., Buning, C., Lengauer, T. (2002) Flexible Docking under Pharmacophore Constraints . Journal of Computer-Aided Molecular Design, 16:129-149.

Rarey, M. (2002) Algorithmen für den computergestützten Wirkstoffentwurf 01. Habilitationsschrift.

Lengauer, T., Lemmen, C., Rarey, M., Zimmermann, M. (2004) Novel technologies for virtual screening . Drug Discovery Today, 9(1):27-34.

Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.-H., Gohla, R., Gossling, F., Grote, K., Heidtke, K., Herrmann, A., O\'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J. O., Lengauer, T., Liebich, I., Linden, M. van der, Luz, H., Meissner, K., Mering, C. von, Mevissen, H.-T., Mewes, H.-W., Michael, H., Mokrejs, M., Muller, T., Pospisil, H., Rarey, M., Reich, J. G., Schneider, R., Schomburg, D., Schulze-Kremer, S., Schwarzer, K., Sommer, I., Springstubbe, S., Suhai, S., Thoppae, G., Vingron, M., Warfsmann, J., Werner, T., Wetzler, D., Wingender, E., Zimmer, R. (2004) The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources . Bioinformatics, 20:268-270.

Rarey, M., Kramer, B., Bernd, C., Lengauer, T. (1996) Time-Efficient Docking of similar flexible ligands . Biocomputing: Proceedings of the 1996 Pacific Symposium (electronic version at http://www.cgl.ucsf.edu/psb/psb96/proceedings/eproceedings.html) (Hunter, L., Klein, T., ed.)

Schellhammer, I., Rarey, M. (2004) FlexX-Scan: Fast Structure-Based Virtual Screening . PROTEINS: Structure, Function, and Genetics, 57:504-517.

Zimmermann, M., Rarey, M., Naumann, T., Matter, H., Hessler, G., Lengauer, T. (2003) Extracting knowledge from high-throughput screening data: towards the generation of biophore models 01. Proceedings of the 14th EuroQSAR 2002 Symposium, Bournemouth UK: Designing Drugs and Crop Protectants: processes, problems and solutions (Ford, M., Livingstone, D., Dearden, J., Van de Waterbeemd, H., ed.). Blackwell Publishing.

Hindle, S. A., Stahl, M., Rarey, M. (2003) Flexible docking under pharmacophore type constraints: application to virtual screening 01. Proceedings of the 14th EuroQSAR 2002 Symposium, Bournemouth UK: Designing Drugs and Crop Protectants: processes, problems and solutions (Ford, M., Livingstone, D., Dearden, J., Van de Waterbeemd, H., ed.). Blackwell Publishing.

Fricker, P., Gastreich, M., Rarey, M. (2004) Automated Drawing of Structural Molecular Formulas under Constraints . Journal of Chemical Information and Computer Sciences, 44(3):1065-1078.

Gastreich, M., Lemmen, C., Briem, H., Rarey, M. (2005) Addressing the Virtual Screening Challenge - The Flex* Approach . In Virtual Screening in Drug Discovery (Alvarez, J., ed.), pp. 25-46. Decker/CRC Press.

Rarey, M., Lemmen, C., Matter, H. (2005) Algorithmic Engines in Virtual Screening . In Cheminformatics in Drug Discovery (Oprea, T. I., Kubinyi, H., Folkers, G., ed.), Vol. 23, pp. 59-115. Wiley-VCH.

Hessler, G., Zimmermann, M., Matter, H., Evers, A., Naumann, T., Lengauer, T., Rarey, M. (2005) Multiple-ligand-based virtual screening: Methods and Applications of the MTree approach . Journal of Medicinal Chemistry, 48(21):6575-6584.

Rarey, M., Maass, P., Hindle, S. A., Metz, G., Rummey, C., Zimmermann, M. (2006) Feature Trees: Theory and Applications from Large-Scale Virtual Screening to Data Analysis . In Pharmacophores and Pharmacophore Search (Langer, T., Hoffmann, R., Kubinyi, H., Folkers, G., ed.), Vol. 32, pp. 81-116. Wiley-VCH.

Rarey, M., Kramer, B., Lengauer, T., Klebe, G. (1996) A Fast Flexible Docking Method using an Incremental Construction Algorithm . Journal of Molecular Biology, 261(3):470--489.

Rarey, M., Degen, J., Reulecke, I. (2005) Docking and Scoring for Structure-Based Drug Design . In Bioinformatics - From Genomes to Therapies (Lengauer, Thomas, ed.), Vol. 2, pp. 541-600. Wiley-VCH.

Griewel, A., Rarey, M. (2005) From greedy to branch & bound and back: Assessing optimization strategies for incremental construction molecular docking tools 01. German Conference on Bioinformatics GCB 2005 (Torda, A., Kurtz, S., Rarey, M., ed.). Gesellschaft für Informatik (GI).

Rarey, M. (2005) Think Combinatorial: Computergestütztes Wirkstoffdesign mit chemischen Fragmenträumen 01. BIOforum, 01(10):56-59.

Kämper, A., Apostolakis, J., Rarey, M., Marian, C.M., Lengauer, T. (2005) Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies . Journal of Chemical Information and Modelling, 46(2):903-911.

Maaß, P., Schulz-Gasch, T., Stahl, M., Rarey, M. (2007) Recore: A fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations . Journal of Chemical Information and Modeling, 47(2):390-399.

Degen, J., Rarey, M. (2006) FlexNovo: Structure-Based Searching in Large Fragment Spaces . ChemMedChem, 1(8):854-868.

Stierand, K., Maaß, P. C., Rarey, M. (2006) Molecular Complexes at a Glance: Automated Generation of two-dimensional Complex Diagrams . Bioinformatics, 22(14):1710-1716.

Griewel, A., Rarey, M. (2006) Computational Molecular Assembly: A Geometric Hashing Approach 01. German Conference on Bioinformatics GCB 2006 (01, ed.). 01.

Schellhammer, I., Rarey, M. (2007) TrixX: Structure-Based Molecule Indexing for Large-Scale Virtual Screening in Sublinear Time . Journal of Computer-Aided Molecular Design, 21(5):223-238.

Lengauer, T., Rarey, M. (1996) Computational Methods for Biomolecular Docking . Current Opinion in Structural Biology, 6:402--406.

Reulecke, I., Lange, G., Albrecht, J., Klein, R., Rarey, M. (2008) Towards an integrated description of hydrogen bonding and dehydration: II. Reducing false positives in virtual screening using the HYDE scoring function . ChemMedChem, 3(6):885-897.

Stierand, K., Rarey, M. (2007) From Modeling to Medicinal Chemistry: Automatic generation of two-dimensional complex diagrams . ChemMedChem, 2(6):853-860.

Paern, J., Degen, J., Rarey, M. (2007) Exploring Fragment Spaces Under Multiple Physicochemical Constraints . Journal of Computer-Aided Molecular Design, 21(6):327-340.

Griewel, A., Rarey, M. (2007) Computational Reconstruction of Macromolecular Assemblies . NIC Workshop 2007 (Hansmann, U., Meinke, J., Mohanty, S., Zimmermann, O., ed.). NIC-Directors.

Seebeck, B., Reulecke, I., Kamper, A., Rarey, M. (2008) Modeling of metal interaction geometries for protein-ligand docking . Proteins, 71(3):1237-1254.

Fischer, J. R., Rarey, M. (2007) SwiFT: an index structure for reduced graph descriptors in virtual screening and clustering . Journal of Chemical Information and Modeling, 47(4):1341-53.

Degen, J., Wegscheid-Gerlach, C., Zaliani, A., Rarey, M. (2008) On the Art of Compiling and Using `Drug-Like` Chemical Fragment Spaces . ChemMedChem, 3:1503-1507.

Schlosser, J., Rarey, M. (2009) Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds . Journal of Chemical Information and Modeling, 49(4):800-809.

Lippert, T., Rarey, M. (2009) Fast automated placement of polar hydrogen atoms in protein-ligand complexes . Journal of Cheminformatics, 1(13)

Fischer, J.R., Lessel, U., Rarey, M. (2010) LoFT: Similarity-Driven Multi-Objective Focused Library Design . Journal of Chemical Information and Modeling, 50(1):1-21.

Griewel, A., Kayer, O., Schlosser, J., Rarey, M. (2009) Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size . Journal of Chemical Information and Modeling, 49(10):2303-2311.

Henzler, A. M., Rarey, M. (2010) In Pursuit of Fully Flexible Protein-Ligand Docking: Modeling the Bilateral Mechanism of Binding . Molecular Informatics, 29(3):164-173.

Henzler, A. M., Rarey, M. (2011) Protein Flexibility in Structure-Based Virtual Screening: From Models to Algorithms . In Methods and Principles in Medicinal Chemistry. Virtual Screening. Principles, Challenges, and Practical Guidelines (Sotriffer, C., ed.), pp. 223-224. Wiley-VCH Verlag GmbH & Co. KGaA.

Rarey, M., Kramer, B., Lengauer, T. (1997) Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention . Journal of Computer-Aided Molecular Design, 11:369--384.

Stierand, K., Rarey, M. (2010) Drawing the PDB - Protein-Ligand Complexes in two Dimensions . Medicinal Chemistry Letters, 1(9):540-545.

Schomburg, K., Ehrlich, H.-C., Stierand, K., Rarey, M. (2010) From Structure Diagrams to Visual Chemical Patterns . Journal of Chemical Information and Modeling, 50(9):1529-1535.

Volkamer, A., Griewel, A., Grombacher, T., Rarey, M. (2010) Analyzing the Topology of Active Sites: On the Prediction of Pockets and Sub-pockets . Journal of Chemical Information and Modeling, 50(11):2041-2052.

Ehrlich, H.-C., Rarey, M. (2011) Maximum common subgraph isomorphism algorithms and their applications in molecular science: a review . WIREs Computational Molecular Science, 1(1):68-79.

Stierand, K., Rarey, M. (2011) Flat and Easy: 2D Depiction of Protein-Ligand Complexes . Molecular Informatics, 30(1):12-19.

Stierand, K., Rarey, M. (2011) Consistent two-dimensional visualization of protein-ligand complex series . Journal of Cheminformatics, 3(21):Online-Publication.

Seebeck, B., Wagener, M., Rarey, M. (2011) From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses . ChemMedChem, 6(9):1630-1639.

Lemcke, T., Dreher, J., Rarey, M., Totzke, F., Schächtele, C., Kubbutat, M. H. G., Kunick, C. (2011) Identification of Inhibitors of the Tyrosine Kinase c-Met by
Structure-Based Virtual Screening . Molecular Informatics, 30(2-3):145-150.

Fischer, J. R., Lessel, U., Rarey, M. (2011) Improving Similarity-Driven Library Design: Customized Matching an Regio-Selective Feature Trees . Journal of Chemical Information and Modeling, 51(9):2156–2163.

Schroeder, M., Kolodzik, A., Windshügel, B., Krepstakies, M., Priyadarshinic, P., Hauber, J., Rarey, M., Meier, C. (2010) Rational Drug Design - Screening and Synthesis of Potential Deoxyhypusine Synthase Inhibitors Targeting HIV-1 Replication .

Zaliani, A., Boda, K., Seidel, T., Herwig, A., Schwab, C. H., Gasteiger, J., Claußen, H., Lemmen, C., Degen, J., Pärn, J., Rarey, M. (2009) Second-generation de novo Design: A view from a medicinal chemist perspective . Journal of Computer-Aided Molecular Design, 23(8):593-602.

Lippert, T., Schulz-Gasch, T., Roche, O., Guba, W., Rarey, M. (2011) De novo design by pharmacophore-based searches in fragment spaces . Journal of Computer-Aided Molecular Design, 25(10):931-945.

Rarey, M. (2011) Some thoughts on the A in computer-aided molecular design . Journal of Computer-Aided Molecular Design, 26(1):113-114.

Schneider, N., Hindle, S., Lange, G., Klein, R., Albrecht, J., Briem, H., Beyer, K., Claußen, H., Gastreich, M., Lemmen, C., Rarey, M. (2011) Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function . Journal of Computer-Aided Molecular Design, 26(6):701-723.

Urbaczek, S., Kolodzik, A., Fischer, J. R., Lippert, T., Heuser, S., Schulz-Gasch, T., Rarey, M. (2011) NAOMI: On the Almost Trivial Task of Reading Molecules
from Different File formats . Journal of Chemical Information and Modeling, 51(12):3199-3207.

Rarey, M. (2012) Author Profile . ChemMedChem, 7(3):355.

Volkamer, A., Kuhn, D., Grombacher, T., Rippmann, F., Rarey, M. (2012) Combining Global and Local Measures for Structure-Based Druggability Predictions . Journal of Chemical Information and Modeling, 52(2):360-372.

Volkamer, A., Kuhn, D., Rippmann, F., Rarey, M. (2012) DoGSiteScorer: A web-server for automatic binding site prediction, analysis, and druggability assessment . Bioinformatics, 28(15):2074–2075.

Schulz-Gasch, T., Schärfer, C., Guba, W., Rarey, M. (2012) TFD: Torsion Fingerprints As a New Measure To Compare Small
Molecule Conformations . Journal of Chemical Information and Modeling, 52(6):1499−1512.

Schneider, N., Klein, R., Lange, G., Rarey, M. (2012) Nearly no Scoring Function without a Hansch-Analysis . Molecular Informatics, 31(6-7):503–507.

Lessel, U., Wellenzohn, B., Fischer, J. R., Rarey, M. (2012) Design of Combinatorial Libraries for the Exploration of Virtual Hits
from Fragment Space Searches with LoFT . Journal of Chemical Information and Modeling, 52(2):373-379.

Ehrlich, H.-C., Rarey, M. (2012) Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2 . Journal of Cheminformatics, 4(13)

Ziegler, P., Chahoud, T., Wilhelm, T., Pällman, N., Braig, M., Wiehle, V., Ziegler, S., Schröder, M., Meier, C., Kolodzik, A., Rarey, M., Panse, J., Hauber, J., Balabanov, S., Brümmendorf, T. H. (2012) Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias . Investigational New Drugs

Schomburg, K. T., Ardao, I., Götz, K., Rieckenberg, F., Liese, A., Zeng, A.-P., M., Rarey. (2012) Computational biotechnology: Prediction of competitive substrate inhibition
of enzymes by buffer compounds with protein-ligand docking . Journal of Biotechnology, 161:391-401.

Heinzerling, L., Klein, R., Rarey, M. (2012) Fast force field-based optimization of protein-ligand complexes with graphics processor . Journal of Computational Chemistry, 33(2):2554-2565.

Meanwell, N.A., Gastreich, M. Rarey, M.,Devereux, M., Popelier, P., Schneider, G., Willet, P. (2012) Perspectives from Medical Chemistry . In Bioisoteres in Medical Chemistry (Nathan Brown, ed.), pp. 217-230. Wiley-VCH .

Stierand, K., Harder, T., Marek, T., Hilbig, M., Lemmen, C., Rarey, M. (2012) The internet as scientific knowledge base: Navigating the chem-bio space . Molecular Informatics:543-546.

Kolodzik, A., Urbaczek, S., Rarey, M. (2012) Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies . Journal of Chemical Information and Modeling, 52(8):2013-2021.

Ehrlich, H.C., Volkamer, A., Rarey, M. (2012) Searching for Substructures in Fragment Spaces . Journal of Chemical Information and Modeling, 52(12):3181-3189.

Urbaczek, S., Kolodzik, A., Heuser, S., Groth, I., Rarey, M. (2013) Reading PDB: Perception of Molecules from 3D Atomic Coordinates . Journal of Chemical Information and Modeling, 53(1):76-87.

Volkamer, A., Kuhn, D., Rippmann, F., Rarey, M. (2013) Predicting enzymatic function from global binding site descriptors . Proteins: Structure, Function and Bioinformatics, 81(3):479-489.

Schneider, N., Lange, G., Hindle, S., Klein, R., Rarey, M. (2013) A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function . Journal of Computer-Aided Molecular Design, 27(1):15-29.

Schomburg, K., Wetzer, L., Rarey, M. (2013) Interactive design of generic chemical patterns . Drug Discovery Today, 13:1-8.

von Behren, M., Volkamer, A., Henzler, A.M., Schomburg, K., Urbaczek, S., Rarey, M. (2013) Fast Protein Binding Site Comparison via an Index-Based Screening Technology . Journal of Chemical Information and Modeling, 53:411-422.

Schomburg, K., Stierand, K., Rarey, M. (2013) Informative Molekulare Visualisierung: Innovative grafische Darstellungen von Molekülmodellen veranschaulichen komplexe Zusammenhänge . BIOspektrum, 2:146-148.

Schärfer, C., Schulz-Gasch, T., Ehrlich, H.C., Guba, W., Rarey, M., Stahl, M. (2013) Torsion Angle Preferences in Drug-like Chemical Space: A Comprehensive Guide . Journal of Medicinal Chemistry, 56 (6):2016-28.

Rarey, M., Schwabe, T. (2013) Jenseits von Google - Chemie im Computer- und Informationszeitalter . Praxis der Naturwissenschaften - Chemie in der Schule, 2(62):5-9.

Ehrlich, H.-C., Henzler, A.M., Rarey, M. (2013) Searching for Recursively Defined Generic Chemical Patterns in Non-Enumerated Fragment Spaces . Journal of Chemical Information and Modeling, 53(7):1676-1688.

Wirth, M., Volkamer, A., Zoete, V., Rippmann, F., Michielin, O., Rarey, M., Sauer, W.H.B. (2013) Protein pocket and ligand shape comparison and its application in virtual screening . Journal of Computer Aided Molecular Design, 27:511-524.

Hilbig, M.; Urbaczek, S.; Groth, I.; Heuser, S.; Rarey, M. (2013) MONA - Interactive manipulation of molecule collections . Journal of Cheminformatics, 5 (38)

Schärfer, C.; Schulz-Gasch, T.; Hert, J.; Heinzerling, L. ; Schulz, B.; Inhester, T.; Stahl, M.; Rarey, M. (2013) CONFECT: Conformations from an Expert Collection of Torsion Patterns . ChemMedChem, 8:1690-1700.

Azzaoui, K.; Jacoby, E.; Senger, S.; Cuadrado Rodríguez, E.; Loza, M.; Zdrazil, B.; Pinto, M.; Williams, A.J.; de la Torre, V.; Mestres, J.; Pastor, M.; Taboureau, O.; Rarey, M.; Chichester, C.; Pettifer, S.; Blomberg, N.; Harland, L.; Williams-Jones, B.; Ecker, G.F. (2013) Scientific competency questions as the basis for semantically enriched open pharmacological space development . Drug Discovery Today, 18(17/18):843-852.

Schröder, M., Kolodzik, A., Pfaff, K., Priyadarshini, P., Krepstakies, M., Hauber, J., Rarey, M., Meier, C. (2014) In silico Design, Synthesis and Screening of Novel Deoxyhypusine Synthase Inhibitors Targeting HIV-1 Replication . ChemMedChem, 9:940-952.

Volkamer, A., Rarey, M. (2014) Exploiting structural information for drug target assessment . Future Medicinal Chemistry, 6(3):319-331.

Urbaczek, S., Kolodzik, A., Rarey, M. (2014) The Valence State Combination Model: A generic framework for handling tautomers and protonation states . Journal of Chemical Information and Modeling, 54(3):756-766.

Bietz, S.; Urbaczek, S.; Schulz, B.; Rarey, M. (2014) Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes . Journal of Cheminformatics, 6(12):1-12.

Schomburg, K.T.; Bietz, S.; Briem, H.; Henzler, A.M.; Urbaczek, S.; Rarey, M. (2014) Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening . Journal of Chemical Information and Modeling, 54(6):1676-1686.

Henzler, A.M., Urbaczek, S., Hilbig, M., Rarey, M. (2014) An integrated approach to knowledge-driven structure-based virtual screening . Journal of Computer-Aided Molecular Design, 28(9):927-39.

Inhester, T., Rarey, M. (2014) Protein-Ligand Interaction Databases: Advanced Tools to Mine Activity Data and Interactions on a Structural Level . WIREs Computational Molecular Science, 4(6):562-575.

Schomburg, K.T.; Rarey, M. (2014) Benchmark Data Sets for Structure-Based Computational Target Prediction . Journal of Chemical Information and Modeling, 54(8):2261-2274.

Schomburg, K., Rarey, M. (2014) What is the potential of structure-based target prediction methods? . Future Medicinal Chemistry, 6(18):1987 - 1989.

Nittinger, E.; Schneider, N.; Lange, G.; Rarey, M. (2015) Evidence of Water Molecules—A Statistical Evaluation of Water Molecules Based on Electron Density . Journal of Chemical Information and Modeling, 55(4):771 - 783.

Schneider,N.; Volkamer,A.; Nittinger,E.; Rarey, M. (2015) Supporting Biocatalysis Research with Structural Bioinformatics . In Applied Biocatalysis: From Fundamental Science to Industrial Applications (in press) ( Liese, A.; Hilterhaus, L.; Kettling, U.; Antranikian, G. , ed.). Wiley-VCH.

Wagener, M.; Oellien, F.; Fechner, U.; Rarey, M. (2015) 10th ICCS/GCC Conference: 40 Years of Cheminformatics . Journal of Chemical Information and Modeling, 55(6):1087.

Bietz, S.; Rarey, M. (2015) ASCONA: Rapid Detection and Alignment of Protein Binding Site
Conformations . Journal of Chemical Information and Modeling, 55(8):1747–1756.

Bietz, S.; Schomburg, K. T.; Hilbig, M.; Rarey, M. (2015) Discriminative Chemical Patterns: Automatic and Interactive Design . Journal of Chemical Information and Modeling, 55(8):1535–1546.

Matthias Hilbig;
Matthias Rarey (2015) MONA 2: A Light Cheminformatics Platform for Interactive
Compound Library Processing . Journal of Chemical Information and Modeling, 55(10):2071–2078.

Guba, W.; Meyder, A.; Rarey, M.; Hert, J. (2016) Torsion Library Reloaded: A New Version of Expert-Derived SMARTS rules
for Assessing Conformations of Small Molecules . Journal of Chemical Information and Modeling, 56(1):1-5.

Lang, T.; Flachsenberg, F.; von Luxburg, U.; Rarey, M. (2016) Feasibility of Active Machine Learning for Multiclass Compound
Classification . Journal of Chemical Information and Modeling, 56(1):12-20.

Bietz, S.; Rarey, M. (2016) SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles . Journal of Chemical Information and Modeling, 56(1):248-59.

Bietz, S.; Fährrolfes, R.; Rarey, M. (2016) The Art of Compiling Protein Binding Site Ensembles . Molecular Informatics, 35(11/12):593-598.

Sommer, K.; Friedrich, N.-O.; Bietz, S.; Hilbig, M.; Inhester, T.; Rarey, M: (2016) UNICON: A powerful and easy-to-use compound library converter . Journal of Chemical Information and Modeling, 56(6):1105–1111.

Lauck, F.; Rarey, M. (2016) FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption . Journal of Chemical Information and Modeling, 56(9):1641-1653.

von Behren, M.; Bietz, S.; Nittinger, E.; Rarey, M. (2016) mRAISE: an alternative algorithmic approach to ligand-based virtual screening . Journal of Computer-Aided Molecular Design, 30(8):583-594.

Lauck, Florian; Rarey, Matthias (2013) Coping with Combinatorial Space in Molecular Design . In De novo Molecular Design, pp. 325-347

Inhester, T.; Bietz, S.; Hilbig, M.; Schmidt, R., Rarey, M. (2017) Index-based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces . Journal of Chemical Information and Modeling, 57(2):148-158.

Flachsenberg, F.; Andresen, N.; Rarey, M. (2017) RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases . Journal of Chemical Information and Modeling, 57(2):122-126.

Friedrich, N.-O.; Meyder, A.; Sommer, K.; Flachsenberg, F.; de Bruyn Kops, C.; Rarey, M.; Kirchmair, J. (2017) High-quality dataset of protein-bound ligand conformations and its application to benchmarking conformer ensemble generators . Journal of Chemical Information and Modeling, 57(3):529-539.

von Behren, M.; Rarey, M. (2017) Ligand-based Virtual Screening under Partial Shape Constraints . Journal of Computer-Aided Molecular Design, 31 (4):335-347.

Schomburg, K.T.; Nittinger, E.; Meyder, A.; Bietz,S.; Schneider, N.; Lange, G.; Klein, R.; Rarey, M. (2017) Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study . Proteins, 85(8):1550-1566.

Nittinger, E.; Inhester, T.; Bietz, S.; Meyder, A.; Schomburg, K.T.; Lange, G.; Klein, R.; Rarey, M. (2017) A Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces . Journal of Medicinal Chemistry, 60:4245-4257.

Fährrolfes, R.; Bietz, S.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Otto, T.; Volkamer, A.; Rarey, M. (2017) ProteinsPlus: a web portal for structure analysis of macromolecules . Nucleic Acids Research, 45:W337-W343.

Bietz, S.; Inhester, T.; Lauck, F.; Sommer, K.; von Behren, M.; Fährrolfes, R.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Otto, T.; Hilbig, M.; Schomburg, K.; Volkamer, A.; Rarey, M. (2017) From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library . Journal of Biotechnology, 261:207-214.

Inhester, T.; Nittinger, E.; Sommer, K.; Schmidt, P.; Bietz, S.; Rarey, M. (2017) NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures . Journal of Chemical Information and Modeling, 57(9):2132–2142.

Meyder, A.; Nittinger, E.; Lange, G.; Klein, R.; Rarey, M. (2017) Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures . Journal of Chemical Information and Modeling, 57(10):2437–2447.

Wagner, V.; Jantz, L.; Briem, H.; Sommer, K.; Rarey, M., Christ, C. (2017) Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation . ChemMedChem, 12(22):1866-1872.

Friedrich, N.-O.; de Bruyn Kops, Christina; Flachsenberg, F.; Sommer, K.; Rarey, M.; Kirchmair, J. (2017) Benchmarking Commercial Conformer Ensemble Generators . Journal of Chemical Information and Modeling, 57(11):2719-2728.

Ehmki, E.S.R.; Rarey, M. (2018) Exploring Structure-Activity Relationships with Three-Dimensional Matched Molecular Pairs - A Review . ChemMedChem, 13(6):482-489.

Nittinger, E.; Flachsenberg, F.; Bietz, S.; Lange, G.; Klein, R.; Rarey, M. (2018) Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples . Journal of Chemical Information and Modeling, 58(8):1625-1637.

Hochreiter, S.; Klambauer, G.; Rarey, M. (2018) Machine Learning in Drug Discovery . Journal of Chemical Information and Modeling, 58(9):1723-1724.

Meyder, A.; Kampen, S.; Sieg, J.; Fährrolfes, R.; Friedrich, N.-O.; Flachsenberg, F.; Rarey, M. (2018) StructureProfiler: An all-in-one Tool for 3D Protein Structure Profiling . Bioinformatics, 35(5):874-876.

Sommer, K.; Flachsenberg, F.; Rarey, M. (2018) NAOMInext - Synthetically feasible fragment growing in a structure-based design context . European Journal of Medicinal Chemistry, 163:747-762.

Friedrich, N.-O.; Flachsenberg, F.; Meyder, A.; Sommer, K.; Kirchmair, J.; Rarey, M. (2019) Conformator: A Novel Method for the Generation of Conformer Ensembles . Journal of Chemical Information and Modeling, 59(2):731-742.

Sieg, J.; Flachsenberg, F.; Rarey, M. (2019) In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening . Journal of Chemical Information and Modeling(59):947-961.

Schmidt, R.; Ehmki, E.S.R.; Ohm, F.; Ehrlich, H.-C.; Mashychev, A.; Rarey, M. (2019) Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms . Journal of Chemical Information and Modeling, 59(6):2560-2571.

Ehmki, E.S.R.; Schmidt, R.; Ohm, F.; Rarey, M. (2019) Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis . Journal of Chemical Information and Modeling, 59(6):2572-2586.

Bellmann, L.; Penner, P.; Rarey, M. (2019) Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration . Journal of Chemical Information and Modeling, 59 (11):4625-4635.

Volkamer, A.; von Behren, M.; Bietz, S.; Rarey, M. (2018) Prediction, Analysis, and Comparison of Active Sites . In Applied Cheminformatics - Achievements and Future Opportunities. Wiley.

Kolodzik, A., Schneider, N.; Rarey, M. (2018) Structure-Based Virtual Screening . In Applied Cheminformatics - Achievements and Future Opportunities. Wiley.

Schöning-Stierand, K.; Diedrich, K.; Fährrolfes, R.; Flachsenberg, F.; Meyder, A.; Nittinger, E.; Steinegger, R.; Rarey, M. (2020) ProteinsPlus: interactive analysis of protein–ligand binding interfaces . Nucleic Acids Research, 48(W1):W48-W53.

Orengo, C.; Velankar, S.; Wodak, S.; Zoete, V.; Bonvin, A.M.J.J.; Elofsson, A.; Feenstra, K.A.; Gerloff, D.L., Hamelryck, T.; Hancock, J.M.; Helmer-Citterich, M.; Hospital, A.; Orozco, M.; Perrakis, A.; Rarey, M.; Soares, C.; Sussmann, J.L.; Thornton, J.M.; Tuffery, P.; Tusnady, G.; Wierenga, R.; Salminen, T.; Schneider, B. (2020) A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community) . F1000Research

Diedrich, K.; Graef, J.; Schöning-Stierand, K.; Rarey, M. (2020) GeoMine: interactive pattern mining of protein–ligand interfaces in the Protein Data Bank . Bioinformatics, 37(3):424-425.

Bellmann, L.; Penner, P.; Rarey, M. (2021) Topological Similarity Search in Large Combinatorial Fragment Spaces . Journal of Chemical Information and Modeling, 61(1):238-251.

Flachsenberg, F.; Meyder, A.; Sommer, K.; Penner, P.; Rarey, M. (2020) A Consistent Scheme for Gradient-Based Optimization of Protein–Ligand Poses . Journal of Chemical Information and Modeling

Schmidt, R.; Krull, F.; Heinzke, A.L.; Rarey, M. (2020) Disconnected Maximum Common Substructures under Constraints . Journal of Chemical Information and Modeling, 61(1):167-178.

Penner, P.; Martiny, V.; Gohier, A.; Gastreich, M.; Ducrot, P.; Brown, D.; Rarey, M. (2020) Shape-Based Descriptors for Efficient Structure-Based FragmentGrowing . Journal of Chemical Information and Modeling, 60:6269-6281.

Ehrt, C.; Krause, B.; Schmidt, R.; Ehmki, E.; Rarey, M. (2020) SMARTS.plus – A Toolbox for Chemical Pattern Design . Molecular Informatics, 39(12)

Flachsenberg, F.; Meyder, A.; Sommer, K.; Penner, P.; Rarey, M. (2012) A Consistent Scheme for Gradient-Based Optimization of Protein–Ligand Poses . Journal of Chemical Information and Modeling, 60(12):6502–6522.

Günther, S., Reinke, P.Y.A. et al (2021) Report X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease . Science, 372(6542):642-646.

Flachsenberg, F.; Rarey, M. (2021) LSLOpt: An open‐source implementation of the step‐length controlled LSL‐BFGS algorithm . Journal of Computational Chemistry, 42:1095-1100.

Graef, J.; Ehrt, C.; Diedrich, K.; Poppinga, M.; Ritter, N.; Rarey, M. (2021) Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures . Journal of Medicinal Chemistry, 65(2):1384-1395.

Schmidt, R.; Klein, R.; Rarey, M. (2021) Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces . Journal of Chemical Information and Modeling, 62(9):2133–2150.

Günther, S.; Reinke, P.Y.A. et al (2021) X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease . Science, 372(6542):642-646.

Bellmann, L.; Penner, P.; Gastreich, M.; Rarey, M. (2022) Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs . Journal of Chemical Information and Modeling, 62(3):553–566.

Penner, P.; Guba, W.; Schmidt, R.; Meyder, A.; Stahl, M.; Rarey, M. (2022) The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare . Journal of Chemical Information and Modeling, 62(7):1644–1653.

Sieg, J.; Sandmeier, C.C.; Meents, A.; Lemmen, C.; Streit, W.R.; Rarey, M. (2022) Analyzing structural features of proteins from deep-sea organisms . Proteins: Structure, Function, and Bioinformatics, 90(8):1521-1537.

Warr, W.A.; Nicklaus, M.C.; Nicolaou, C.A.; Rarey, M. (2022) Exploration of Ultralarge Compound Collections for Drug Discovery . Journal of Chemical Information and Modeling, 62(9):2021–2034.

Schöning-Stierand, K.; Diedrich, K.; Ehrt, C.; Flachsenberg, F.; Graef, J.; Sieg, J.; Penner, P.; Poppinga, M.; Ungethüm, A.; Rarey, M. (2022) ProteinsPlus: a comprehensive collection of web-based molecular modeling tools . Nucleic Acids Research, 50(1):W611-W615.

Bellmann, L.; Klein, R.; Rarey, M. (2022) Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces . Journal of Chemical Information and Modeling, 62(11):2800-2810.

Harren, T.; Matter, H.; Hessler, G.; Rarey, M.; Grebner, C. (2022) Interpretation of Structure–Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence . Journal of Chemical Information and Modeling, 62(3):447-462.

Dolfus, U.; Briem, H.; Rarey, M. (2021) Synthesis-Aware Generation of Structural Analogues . Journal of Chemical Information and Modeling, 62(15):3565–3576.

Penner, P.; Martiny, V.; Bellmann, L.; Flachsenberg, F.; Gastreich, M.; Theret, I., Meyer, C.; Rarey, M. (2022) FastGrow: on‑the‑fly growing and its application to DYRK1A . Journal of Computer-Aided Molecular Design, 36(9)(639-651)

Hönig, S.M.N.; Lemmen, C.; Rarey, M. (2022) Small molecule superposition: A comprehensive overview on pose scoring of the latest methods . WIREs Computational Molecular Science

Meyenburg, C.; Dolfus, U.; Briem, H.; Rarey, M. (2022) Galileo: Three‑dimensional searching in large combinatorial fragment spaces on the example of pharmacophores . Journal of Computer-Aided Molecular Design, 37:1-16.

Hönig, S.M.N.; Lemmen, C.; Rarey, M. (2023) Small molecule superposition: A comprehensive overview on pose scoring of the latest methods . WIREs Computational Molecular Science

Gutermuth, T.; Sieg, J.; Stohn, T.; Rarey, M. (2023) Modeling with Alternate Locations in X-ray Protein Structures . Journal of Chemical Information and Modeling

Graef, J.; Ehrt, C.; Rarey, M. (2023) Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3 . Journal of Chemical Information and Modeling, 63(10):3128-3137.

Pletzer-Zelgert, J.; Ehrt, C.; Fender, I.; Griewel, A.; Flachsenberg, F.; Klebe, G.; Rarey, M. (2023) LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments . Structural Biology, 79(9):837-856.

Diedrich, K.; Krause, B.; Berg, O.; Rarey, M. (2023) PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams . Journal of Computer-Aided Molecular Design, 37:491–503.

Gonzalez-Ponce, K.; Horta Andrade, C.; Hunter, F.; Kirchmair, J.; Martinez-Mayorga, K.; Medina-Franco, J.L.; Rarey, M.; Tropsha, A.; Varnek, A.; Zdrazil, B. (2023) School of cheminformatics in Latin America . Journal of Cheminformatics, 15(82)

Sieg, J. ; Rarey, M. (2023) Searching similar local 3D micro-environments in protein structure databases with MicroMiner . Briefings in Bioinformatics, 24(6)

Flachsenberg, F.; Ehrt, C.; Gutermuth, T.; Rarey, M. (2023) Redocking the PDB . Journal of Chemical Information and Modeling, 64(2):219-237.

Korn, M.; Ehrt, C.; Ruggiu, F.; Gastreich, M.; Rarey, M. (2023) Navigating large chemical spaces in early-phase drug discovery . Current Opinion in Structural Biology, 80(102578)

Reim, T.; Ehrt, C.; Graef, J.; Günther, S.; Meents; Rarey, M. (2024) SiteMine: Large-scale binding site similarity searching in protein structure databases . Archiv der Pharmazie, 357(5)

Poppinga, M.; Graef, J.; Diedrich, K.; Rarey, M., Ritter, N. (2024) Database and Workflow Optimizations for Spatial-Geometric Queries in GeoMine .

Graef, J.; Ehrt, C.; Reim, T.; Rarey, M. (2024) Database-Driven Identification of Structurally Similar Protein-Protein Interfaces . Journal of Chemical Information and Modeling

Lübbers, J.; Lessel, U.; Rarey, M. (2024) Enhanced Calculation of Property Distributions in Chemical Fragment Spaces . Journal of Chemical Information and Modeling

Harren, T.; Gutermuth, T.; Grebner, C.; Hessler, G.; Rarey, M. (2024) Modern machine-learning for binding affinity estimation of protein-ligand complexes: Progress, opportunities, and challenges . WIREs Computational Molecular Science

Ungethüm, A.; Poppinga, M.; Kögel, K.; Rarey, M. (2024) SciFi - Increasing Database Adaptation in Data Science with an Embedded Asset Store . Lernen, Wissen, Daten, Analysen, Conference Proceedings Würzburg