Matthias Rarey

134 papers A 1Misc 1Journal 125Unranked 4

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data. J. Chem. Inf. Model. Emanuel S. R. Ehmki, Torben Gutermuth, Tobias Harren, Stefan Kurtz, Matthias Rarey
2026	J	`jnl`	Guiding Similarity Search in Chemical Fragment Spaces with Weighted Fingerprints. J. Chem. Inf. Model. Justin Lübbers, Malte Schokolowski, Uta F. Lessel, Alexander Weber, Matthias Rarey
2025	Misc	`conf`	Caching Partition Identifiers for Fast Geometric Pattern Matching. BTW Martin Poppinga, Annett Ungethüm, Matthias Rarey
2025	J	`jnl`	Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays. J. Comput. Aided Mol. Des. Sophia M. N. Hönig, Torben Gutermuth, Christiane Ehrt, Christian Lemmen, Matthias Rarey
2025	J	`jnl`	SmartChemist─Simplifying Communication About Organic Chemical Structures. J. Chem. Inf. Model. Torben Gutermuth, Patrick Penner, Jochen Sieg, Uschi Dolfus, Matthias Rarey
2024	J	`jnl`	Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. J. Chem. Inf. Model. Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
2024	J	`jnl`	Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. J. Chem. Inf. Model. Justin Lübbers, Uta F. Lessel, Matthias Rarey
2024	J	`jnl`	Redocking the PDB. J. Chem. Inf. Model. Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey
2024	J	`jnl`	SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. J. Comput. Aided Mol. Des. Sophia M. N. Hönig, Florian Flachsenberg, Christiane Ehrt, Alexander Neumann, Robert Schmidt, Christian Lemmen, Matthias Rarey
2024	J	`jnl`	User-centric design of a 3D search interface for protein-ligand complexes. J. Comput. Aided Mol. Des. Konrad Diedrich, Christiane Ehrt, Joel Graef, Martin Poppinga, Norbert Ritter, Matthias Rarey
2023	J	`jnl`	Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. J. Chem. Inf. Model. Joel Graef, Christiane Ehrt, Matthias Rarey
2023	—	`conf`	Database and Workflow Optimizations for Spatial-Geometric Queries in GeoMine. LWDA Martin Poppinga, Joel Graef, Konrad Diedrich, Matthias Rarey, Norbert Ritter
2023	J	`jnl`	Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures. J. Chem. Inf. Model. Uschi Dolfus, Hans Briem, Torben Gutermuth, Matthias Rarey
2023	J	`jnl`	Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores. J. Comput. Aided Mol. Des. Christian Meyenburg, Uschi Dolfus, Hans Briem, Matthias Rarey
2023	J	`jnl`	Modeling with Alternate Locations in X-ray Protein Structures. J. Chem. Inf. Model. Torben Gutermuth, Jochen Sieg, Tim Stohn, Matthias Rarey
2023	J	`jnl`	PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J. Comput. Aided Mol. Des. Konrad Diedrich, Bennet Krause, Ole Berg, Matthias Rarey
2023	J	`jnl`	School of cheminformatics in Latin America. J. Cheminformatics Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona M. I. Hunter, Johannes Kirchmair, Karina Martínez-Mayorga, José L. Medina-Franco, Matthias Rarey, Alexander Tropsha, Alexandre Varnek, Barbara Zdrazil
2023	J	`jnl`	Searching similar local 3D micro-environments in protein structure databases with MicroMiner. Briefings Bioinform. Jochen Sieg, Matthias Rarey
2022	J	`jnl`	Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces. J. Chem. Inf. Model. Louis Bellmann, Raphael Klein, Matthias Rarey
2022	J	`jnl`	Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. J. Chem. Inf. Model. Louis Bellmann, Patrick Penner, Marcus Gastreich, Matthias Rarey
2022	J	`jnl`	Exploration of Ultralarge Compound Collections for Drug Discovery. J. Chem. Inf. Model. Wendy A. Warr, Marc C. Nicklaus, Christos A. Nicolaou, Matthias Rarey
2022	J	`jnl`	FastGrow: on-the-fly growing and its application to DYRK1A. J. Comput. Aided Mol. Des. Patrick Penner, Virginie Y. Martiny, Louis Bellmann, Florian Flachsenberg, Marcus Gastreich, Isabelle Theret, Christophe Meyer, Matthias Rarey
2022	J	`jnl`	Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence. J. Chem. Inf. Model. Tobias Harren, Hans Matter, Gerhard Hessler, Matthias Rarey, Christoph Grebner
2022	J	`jnl`	Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. J. Chem. Inf. Model. Robert Schmidt, Raphael Klein, Matthias Rarey
2022	J	`jnl`	Proteins Nucleic Acids Res. Katrin Schöning-Stierand, Konrad Diedrich, Christiane Ehrt, Florian Flachsenberg, Joel Graef, Jochen Sieg, Patrick Penner, Martin Poppinga, Annett Ungethüm, Matthias Rarey
2022	J	`jnl`	Special Issue on Reaction Informatics and Chemical Space. J. Chem. Inf. Model. Matthias Rarey, Marc C. Nicklaus, Wendy A. Warr
2022	J	`jnl`	Synthesis-Aware Generation of Structural Analogues. J. Chem. Inf. Model. Uschi Dolfus, Hans Briem, Matthias Rarey
2022	J	`jnl`	The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. J. Chem. Inf. Model. Patrick Penner, Wolfgang Guba, Robert Schmidt, Agnes Meyder, Martin Stahl, Matthias Rarey
2022	J	`jnl`	Visualizing Generic Reaction Patterns. J. Chem. Inf. Model. Uschi Dolfus, Hans Briem, Matthias Rarey
2021	J	`jnl`	Call for Papers for the Special Issue: From Reaction Informatics to Chemical Space. J. Chem. Inf. Model. Matthias Rarey, Marc C. Nicklaus, Wendy A. Warr
2021	J	`jnl`	Disconnected Maximum Common Substructures under Constraints. J. Chem. Inf. Model. Robert Schmidt, Florian Krull, Anna Lina Heinzke, Matthias Rarey
2021	J	`jnl`	GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank. Bioinform. Konrad Diedrich, Joel Graef, Katrin Schöning-Stierand, Matthias Rarey
2021	J	`jnl`	LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. J. Comput. Chem. Florian Flachsenberg, Matthias Rarey
2021	J	`jnl`	Topological Similarity Search in Large Combinatorial Fragment Spaces. J. Chem. Inf. Model. Louis Bellmann, Patrick Penner, Matthias Rarey
2020	J	`jnl`	A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. J. Chem. Inf. Model. Florian Flachsenberg, Agnes Meyder, Kai Sommer, Patrick Penner, Matthias Rarey
2020	J	`jnl`	Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
2020	J	`jnl`	Proteins Nucleic Acids Res. Katrin Schöning-Stierand, Konrad Diedrich, Rainer Fährrolfes, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Ruben Steinegger, Matthias Rarey
2020	J	`jnl`	Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. J. Chem. Inf. Model. Patrick Penner, Virginie Y. Martiny, Arnaud Gohier, Marcus Gastreich, Pierre Ducrot, David Brown, Matthias Rarey
2019	J	`jnl`	Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis. J. Chem. Inf. Model. Emanuel S. R. Ehmki, Robert Schmidt, Farina Ohm, Matthias Rarey
2019	J	`jnl`	Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms. J. Chem. Inf. Model. Robert Schmidt, Emanuel S. R. Ehmki, Farina Ohm, Hans-Christian Ehrlich, Andriy Mashychev, Matthias Rarey
2019	J	`jnl`	Conformator: A Novel Method for the Generation of Conformer Ensembles. J. Chem. Inf. Model. Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey
2019	J	`jnl`	Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration. J. Chem. Inf. Model. Louis Bellmann, Patrick Penner, Matthias Rarey
2019	J	`jnl`	In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. J. Chem. Inf. Model. Jochen Sieg, Florian Flachsenberg, Matthias Rarey
2019	J	`jnl`	Machine Learning in Drug Discovery. J. Chem. Inf. Model. Günter Klambauer, Sepp Hochreiter, Matthias Rarey
2019	J	`jnl`	StructureProfiler: an all-in-one tool for 3D protein structure profiling. Bioinform. Agnes Meyder, Stefanie Kampen, Jochen Sieg, Rainer Fährrolfes, Nils-Ole Friedrich, Florian Flachsenberg, Matthias Rarey
2018	J	`jnl`	Machine Learning in Drug Discovery. J. Chem. Inf. Model. Sepp Hochreiter, Günter Klambauer, Matthias Rarey
2018	J	`jnl`	Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. J. Chem. Inf. Model. Eva Nittinger, Florian Flachsenberg, Stefan Bietz, Gudrun Lange, Robert Klein, Matthias Rarey
2017	J	`jnl`	Benchmarking Commercial Conformer Ensemble Generators. J. Chem. Inf. Model. Nils-Ole Friedrich, Christina de Bruyn Kops, Florian Flachsenberg, Kai Sommer, Matthias Rarey, Johannes Kirchmair
2017	J	`jnl`	Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. J. Chem. Inf. Model. Agnes Meyder, Eva Nittinger, Gudrun Lange, Robert Klein, Matthias Rarey
2017	J	`jnl`	High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. J. Chem. Inf. Model. Nils-Ole Friedrich, Agnes Meyder, Christina de Bruyn Kops, Kai Sommer, Florian Flachsenberg, Matthias Rarey, Johannes Kirchmair
2017	J	`jnl`	Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces. J. Chem. Inf. Model. Therese Inhester, Stefan Bietz, Matthias Hilbig, Robert Schmidt, Matthias Rarey
2017	J	`jnl`	Ligand-based virtual screening under partial shape constraints. J. Comput. Aided Mol. Des. Mathias M. von Behren, Matthias Rarey
2017	J	`jnl`	ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res. Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey
2017	J	`jnl`	RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. J. Chem. Inf. Model. Florian Flachsenberg, Niek Andresen, Matthias Rarey
2016	J	`jnl`	FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption. J. Chem. Inf. Model. Florian Lauck, Matthias Rarey
2016	J	`jnl`	Feasibility of Active Machine Learning for Multiclass Compound Classification. J. Chem. Inf. Model. Tobias Lang, Florian Flachsenberg, Ulrike von Luxburg, Matthias Rarey
2016	J	`jnl`	SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. J. Chem. Inf. Model. Stefan Bietz, Matthias Rarey
2016	J	`jnl`	Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules. J. Chem. Inf. Model. Wolfgang Guba, Agnes Meyder, Matthias Rarey, Jérôme Hert
2016	J	`jnl`	UNICON: A Powerful and Easy-to-Use Compound Library Converter. J. Chem. Inf. Model. Kai Sommer, Nils-Ole Friedrich, Stefan Bietz, Matthias Hilbig, Therese Inhester, Matthias Rarey
2016	J	`jnl`	mRAISE: an alternative algorithmic approach to ligand-based virtual screening. J. Comput. Aided Mol. Des. Mathias M. von Behren, Stefan Bietz, Eva Nittinger, Matthias Rarey
2015	J	`jnl`	10th ICCS/GCC Conference: 40 Years of Cheminformatics. J. Chem. Inf. Model. Markus Wagener, Frank Oellien, Uli Fechner, Matthias Rarey
2015	J	`jnl`	ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. J. Chem. Inf. Model. Stefan Bietz, Matthias Rarey
2015	J	`jnl`	Discriminative Chemical Patterns: Automatic and Interactive Design. J. Chem. Inf. Model. Stefan Bietz, Karen T. Schomburg, Matthias Hilbig, Matthias Rarey
2015	J	`jnl`	Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density. J. Chem. Inf. Model. Eva Nittinger, Nadine Schneider, Gudrun Lange, Matthias Rarey
2015	J	`jnl`	Letter from the Editors. J. Chem. Inf. Model. Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab
2015	J	`jnl`	MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing. J. Chem. Inf. Model. Matthias Hilbig, Matthias Rarey
2014	J	`jnl`	Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web. J. Cheminformatics Katrin Stierand, Tim Harder, Lothar Wissler, Christian Lemmen, Matthias Rarey
2014	J	`jnl`	An integrated approach to knowledge-driven structure-based virtual screening. J. Comput. Aided Mol. Des. Angela M. Henzler, Sascha Urbaczek, Matthias Hilbig, Matthias Rarey
2014	J	`jnl`	Benchmark Data Sets for Structure-Based Computational Target Prediction. J. Chem. Inf. Model. Karen Schomburg, Matthias Rarey
2014	J	`jnl`	Elucidating protein-protein interactions using the HYDE scoring function. J. Cheminformatics Eva Vennmann, Nadine Schneider, Gudrun Lange, Matthias Rarey
2014	J	`jnl`	Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening. J. Chem. Inf. Model. Karen Schomburg, Stefan Bietz, Hans Briem, Angela M. Henzler, Sascha Urbaczek, Matthias Rarey
2014	J	`jnl`	Facing the challenges of computational target prediction. J. Cheminformatics Karen T. Schomburg, Matthias Rarey
2014	J	`jnl`	Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. J. Cheminformatics Stefan Bietz, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey
2014	J	`jnl`	The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States. J. Chem. Inf. Model. Sascha Urbaczek, Adrian Kolodzik, Matthias Rarey
2013	J	`jnl`	A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. J. Comput. Aided Mol. Des. Nadine Schneider, Gudrun Lange, Sally A. Hindle, Robert Klein, Matthias Rarey
2013	J	`jnl`	Fast Protein Binding Site Comparison via an Index-Based Screening Technology. J. Chem. Inf. Model. Mathias M. von Behren, Andrea Volkamer, Angela M. Henzler, Karen Schomburg, Sascha Urbaczek, Matthias Rarey
2013	J	`jnl`	Force-field-based minimizations of protein-ligand complexes in the blink of an eye. J. Cheminformatics Lennart Heinzerling, Matthias Rarey
2013	J	`jnl`	Let's talk about rings. J. Cheminformatics Matthias Rarey, Adrian Kolodzik, Sascha Urbaczek
2013	J	`jnl`	MONA - Interactive manipulation of molecule collections. J. Cheminformatics Matthias Hilbig, Sascha Urbaczek, Inken Groth, Stefan Heuser, Matthias Rarey
2013	J	`jnl`	Protein pocket and ligand shape comparison and its application in virtual screening. J. Comput. Aided Mol. Des. Matthias Wirth, Andrea Volkamer, Vincent Zoete, Friedrich Rippmann, Olivier Michielin, Matthias Rarey, Wolfgang H. B. Sauer
2013	J	`jnl`	Reading PDB: Perception of Molecules from 3D Atomic Coordinates. J. Chem. Inf. Model. Sascha Urbaczek, Adrian Kolodzik, Inken Groth, Stefan Heuser, Matthias Rarey
2013	J	`jnl`	Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces. J. Chem. Inf. Model. Hans-Christian Ehrlich, Angela M. Henzler, Matthias Rarey
2013	J	`jnl`	TorsionAnalyzer: exploring conformational space. J. Cheminformatics Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey
2012	J	`jnl`	A flexible-hydrogen interaction model for protein-ligand docking. J. Cheminformatics Angela M. Henzler, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey
2012	J	`jnl`	Aligning chemical structure diagrams with local search. J. Cheminformatics Matthias Hilbig, Matthias Rarey
2012	J	`jnl`	Combining Global and Local Measures for Structure-Based Druggability Predictions. J. Chem. Inf. Model. Andrea Volkamer, Daniel Kuhn, Thomas Grombacher, Friedrich Rippmann, Matthias Rarey
2012	J	`jnl`	Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT. J. Chem. Inf. Model. Uta F. Lessel, Bernd Wellenzohn, J. Robert Fischer, Matthias Rarey
2012	J	`jnl`	DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinform. Andrea Volkamer, Daniel Kuhn, Friedrich Rippmann, Matthias Rarey
2012	J	`jnl`	Fast force field-based optimization of protein-ligand complexes with graphics processor. J. Comput. Chem. Lennart Heinzerling, Robert Klein, Matthias Rarey
2012	J	`jnl`	Searching for Substructures in Fragment Spaces. J. Chem. Inf. Model. Hans-Christian Ehrlich, Andrea Volkamer, Matthias Rarey
2012	J	`jnl`	Some thoughts on the "A" in computer-aided molecular design. J. Comput. Aided Mol. Des. Matthias Rarey
2012	J	`jnl`	Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. J. Comput. Aided Mol. Des. Nadine Schneider, Sally A. Hindle, Gudrun Lange, Robert Klein, Jürgen Albrecht, Hans Briem, Kristin Beyer, Holger Claußen, Marcus Gastreich, Christian Lemmen, Matthias Rarey
2012	J	`jnl`	Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2. J. Cheminformatics Hans-Christian Ehrlich, Matthias Rarey
2012	J	`jnl`	Systematic search for pairwise dependencies of torsion angles. J. Cheminformatics Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey
2012	J	`jnl`	TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. J. Chem. Inf. Model. Tanja Schulz-Gasch, Christin Schärfer, Wolfgang Guba, Matthias Rarey
2012	J	`jnl`	Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies. J. Chem. Inf. Model. Adrian Kolodzik, Sascha Urbaczek, Matthias Rarey
2011	J	`jnl`	Chemical pattern visualization in 2D - the SMARTSviewer. J. Cheminformatics Karen Schomburg, Hans-Christian Ehrlich, Katrin Stierand, Matthias Rarey
2011	J	`jnl`	Consistent two-dimensional visualization of protein-ligand complex series. J. Cheminformatics Katrin Stierand, Matthias Rarey
2011	J	`jnl`	De novo design by pharmacophore-based searches in fragment spaces. J. Comput. Aided Mol. Des. Tobias Lippert, Tanja Schulz-Gasch, Olivier Roche, Wolfgang Guba, Matthias Rarey
2011	J	`jnl`	HYDEing the false positives - scoring for lead optimization. J. Cheminformatics Nadine Schneider, Gudrun Lange, Robert Klein, Christian Lemmen, Matthias Rarey
2011	J	`jnl`	Hydrogen placement in protein-ligand complexes under consideration of tautomerism. J. Cheminformatics Stefan Bietz, Sascha Urbaczek, Matthias Rarey
2011	J	`jnl`	Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees. J. Chem. Inf. Model. J. Robert Fischer, Uta F. Lessel, Matthias Rarey
2011	J	`jnl`	NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats. J. Chem. Inf. Model. Sascha Urbaczek, Adrian Kolodzik, J. Robert Fischer, Tobias Lippert, Stefan Heuser, Inken Groth, Tanja Schulz-Gasch, Matthias Rarey
2011	J	`jnl`	Searching substructures in fragment spaces. J. Cheminformatics Hans-Christian Ehrlich, Matthias Rarey
2010	J	`jnl`	Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. J. Chem. Inf. Model. Andrea Volkamer, Axel Griewel, Thomas Grombacher, Matthias Rarey
2010	J	`jnl`	From Structure Diagrams to Visual Chemical Patterns. J. Chem. Inf. Model. Karen Schomburg, Hans-Christian Ehrlich, Katrin Stierand, Matthias Rarey
2010	J	`jnl`	LoFT: Similarity-Driven Multiobjective Focused Library Design. J. Chem. Inf. Model. J. Robert Fischer, Uta F. Lessel, Matthias Rarey
2010	J	`jnl`	PoseView - molecular interaction patterns at a glance. J. Cheminformatics Katrin Stierand, Matthias Rarey
2010	J	`jnl`	Where are the boundaries? Automated pocket detection for druggability studies. J. Cheminformatics Andrea Volkamer, Thomas Grombacher, Matthias Rarey
2009	J	`jnl`	Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. J. Chem. Inf. Model. Jochen Schlosser, Matthias Rarey
2009	J	`jnl`	Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size. J. Chem. Inf. Model. Axel Griewel, Ole Kayser, Jochen Schlosser, Matthias Rarey
2009	J	`jnl`	Fast automated placement of polar hydrogen atoms in protein-ligand complexes. J. Cheminformatics Tobias Lippert, Matthias Rarey
2009	J	`jnl`	Second-generation de novo design: a view from a medicinal chemist perspective. J. Comput. Aided Mol. Des. Andrea Zaliani, Krisztina Boda, Thomas Seidel, Achim Herwig, Christof H. Schwab, Johann Gasteiger, Holger Claussen, Christian Lemmen, Jörg Degen, Juri Pärn, Matthias Rarey
2007	J	`jnl`	Exploring fragment spaces under multiple physicochemical constraints. J. Comput. Aided Mol. Des. Juri Pärn, Jörg Degen, Matthias Rarey
2007	J	`jnl`	Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations. J. Chem. Inf. Model. Patrick C. Maaß, Tanja Schulz-Gasch, Martin Stahl, Matthias Rarey
2007	J	`jnl`	SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering. J. Chem. Inf. Model. J. Robert Fischer, Matthias Rarey
2007	J	`jnl`	TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. J. Comput. Aided Mol. Des. Ingo Schellhammer, Matthias Rarey
2006	J	`jnl`	Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. J. Chem. Inf. Model. Andreas Kämper, Joannis Apostolakis, Matthias Rarey, Christel M. Marian, Thomas Lengauer
2006	J	`jnl`	Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. Bioinform. Katrin Stierand, Patrick C. Maaß, Matthias Rarey
2005	—	`conf`	From greedy to branch & bound and back: Assessing optimization strategies for incremental construction molecular docking tools. German Conference on Bioinformatics Axel Griewel, Matthias Rarey
2005	—	`ed.`	Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, Germany, October 5-7, 2005 German Conference on Bioinformatics Andrew Ernest Torda, Stefan Kurtz, Matthias Rarey
2004	J	`jnl`	Automated Drawing of Structural Molecular Formulas under Constraints. J. Chem. Inf. Model. Patrick C. Fricker, Marcus Gastreich, Matthias Rarey
2004	J	`jnl`	The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. Bioinform. 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
2002	J	`jnl`	Flexible docking under pharmacophore type constraints. J. Comput. Aided Mol. Des. Sally A. Hindle, Matthias Rarey, Christian Buning, Thomas Lengauer
2002	—	`conf`	Geometric Problems and Algorithms in Computer-Aided Molecular Design. GI Jahrestagung (Ergänzungsband) Matthias Rarey
2001	—	`book`	Algorithmen für den computergestützten Wirkstoffentwurf. Matthias Rarey
2001	J	`jnl`	Similarity searching in large combinatorial chemistry spaces. J. Comput. Aided Mol. Des. Matthias Rarey, Martin Stahl
1999	J	`jnl`	Docking of hydrophobic ligands with interaction-based matching algorithms. Bioinform. Matthias Rarey, Bernd Kramer, Thomas Lengauer
1998	—	`conf`	Docking of hydrophobic ligands with interaction-based matching algorithms. German Conference on Bioinformatics Matthias Rarey, Bernd Kramer, Thomas Lengauer
1998	J	`jnl`	Feature trees: A new molecular similarity measure based on tree matching. J. Comput. Aided Mol. Des. Matthias Rarey, J. Scott Dixon
1997	J	`jnl`	Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. J. Comput. Aided Mol. Des. Matthias Rarey, Bernd Kramer, Thomas Lengauer
1996	J	`jnl`	Placement of medium-sized molecular fragments into active sites of proteins. J. Comput. Aided Mol. Des. Matthias Rarey, Stephan Wefing, Thomas Lengauer
1996	—	`book`	Rechnergestützte Vorhersage von Rezeptor-Ligand-Wechselwirkungen. Matthias Rarey
1995	A	`conf`	Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins. ISMB Matthias Rarey, Bernd Kramer, Thomas Lengauer