Matthias Rarey

Nadine Schneider, Gudrun Lange, Sally A. Hindle, Robert Klein, Matthias Rarey: 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 (2013)

Andrea Volkamer, Daniel Kuhn, Friedrich Rippmann, Matthias Rarey: DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinformatics 28(15): 2074-2075 (2012)

Matthias Rarey: Some thoughts on the "A" in computer-aided molecular design. Journal of Computer-Aided Molecular Design 26(1): 113-114 (2012)

Nadine Schneider, Sally A. Hindle, Gudrun Lange, Robert Klein, Jürgen Albrecht, Hans Briem, Kristin Beyer, Holger Claußen, Marcus Gastreich, Christian Lemmen, Matthias Rarey: Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. Journal of Computer-Aided Molecular Design 26(6): 701-723 (2012)

Lennart Heinzerling, Robert Klein, Matthias Rarey: Fast force field-based optimization of protein-ligand complexes with graphics processor. Journal of Computational Chemistry 33(32): 2554-2565 (2012)

Hans-Christian Ehrlich, Matthias Rarey: Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2. J. Cheminformatics 4: 13 (2012)

Tobias Lippert, Tanja Schulz-Gasch, Olivier Roche, Wolfgang Guba, Matthias Rarey: De novo design by pharmacophore-based searches in fragment spaces. Journal of Computer-Aided Molecular Design 25(10): 931-945 (2011)

Katrin Stierand, Matthias Rarey: Consistent two-dimensional visualization of protein-ligand complex series. J. Cheminformatics 3: 21 (2011)

Andrea Zaliani, Krisztina Boda, Thomas Seidel, Achim Herwig, Christof H. Schwab, Johann Gasteiger, Holger Claussen, Christian Lemmen, Jörg Degen, Juri Pärn, Matthias Rarey: Second-generation de novo design: a view from a medicinal chemist perspective. Journal of Computer-Aided Molecular Design 23(8): 593-602 (2009)

Tobias Lippert, Matthias Rarey: Fast automated placement of polar hydrogen atoms in protein-ligand complexes. J. Cheminformatics 1: 13 (2009)

Katrin Stierand, Patrick C. Maaß, Matthias Rarey: Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. Bioinformatics 22(14): 1710-1716 (2006)

Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer: Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. Journal of Chemical Information and Modeling 46(2): 903-911 (2006)

Axel Griewel, Matthias Rarey: From greedy to branch & bound and back: Assessing optimization strategies for incremental construction molecular docking tools. German Conference on Bioinformatics 2005: 119-130

Andrew E. Torda, Stefan Kurtz, Matthias Rarey (Eds.): Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, Germany, October 5-7, 2005. LNI 71, GI 2005, isbn 3-88579-400-4

Torsten Crass, Iris Antes, Rico Basekow, Peer Bork, Christian Buning, Maik Christensen, Holger Claussen, Christian Ebeling, Peter Ernst, Valérie Gailus-Durner, Karl-Heinz Glatting, Rolf Gohla, Frank Gößling, Korbinian Grote, Karsten R. Heidtke, Alexander Herrmann, Sean O'Keeffe, O. Kießlich, Sven Kolibal, Jan O. Korbel, Thomas Lengauer, Ines Liebich, Mark van der Linden, Hannes Luz, Kathrin Meissner, Christian von Mering, Heinz-Theodor Mevissen, Hans-Werner Mewes, Holger Michael, Martin Mokrejs, Tobias Müller, Heike Pospisil, Matthias Rarey, Jens G. Reich, Ralf Schneider, Dietmar Schomburg, Steffen Schulze-Kremer, Knut Schwarzer, Ingolf Sommer, Stephan Springstubbe, Sándor Suhai, Gnanasekaran Thoppae, Martin Vingron, Jens Warfsmann, Thomas Werner, Daniel Wetzler, Edgar Wingender, Ralf Zimmer: The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinformatics 20(2): 268-270 (2004)

Patrick C. Fricker, Marcus Gastreich, Matthias Rarey: Automated Drawing of Structural Molecular Formulas under Constraints. Journal of Chemical Information and Modeling 44(3): 1065-1078 (2004)

Sally A. Hindle, Matthias Rarey, Christian Buning, Thomas Lengauer: Flexible docking under pharmacophore type constraints. Journal of Computer-Aided Molecular Design 16(2): 129-149 (2002)

Matthias Rarey: Geometric Problems and Algorithms in Computer-Aided Molecular Design. GI Jahrestagung (Ergänzungsband) 2002: 61-62

Matthias Rarey, Martin Stahl: Similarity searching in large combinatorial chemistry spaces. Journal of Computer-Aided Molecular Design 15(6): 497-520 (2001)

Matthias Rarey, Bernd Kramer, Thomas Lengauer: Docking of hydrophobic ligands with interaction-based matching algorithms. Bioinformatics 15(3): 243-250 (1999)

Matthias Rarey, J. Scott Dixon: Feature trees: A new molecular similarity measure based on tree matching. Journal of Computer-Aided Molecular Design 12(5): 471-490 (1998)

Matthias Rarey, Bernd Kramer, Thomas Lengauer: Docking of hydrophobic ligands with interaction-based matching algorithms. German Conference on Bioinformatics 1998

Matthias Rarey, Bernd Kramer, Thomas Lengauer: Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. Journal of Computer-Aided Molecular Design 11(4): 369-384 (1997)

Matthias Rarey, Stephan Wefing, Thomas Lengauer: Placement of medium-sized molecular fragments into active sites of proteins. Journal of Computer-Aided Molecular Design 10(1): 41-54 (1996)

Matthias Rarey, Bernd Kramer, Thomas Lengauer: Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins. ISMB 1995: 300-308