Matthias Rarey

ORCID

Publication Activity (10 Years)

Years Active: 1995-2024
Publications (10 Years): 61

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

J. Cheminformatics

Nucleic Acids Res.

Publications

Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. J. Chem. Inf. Model. 64 (8) (2024)
Konrad Diedrich, Christiane Ehrt, Joel Graef, Martin Poppinga, Norbert Ritter, Matthias Rarey
User-centric design of a 3D search interface for protein-ligand complexes. J. Comput. Aided Mol. Des. 38 (1) (2024)
Sophia M. N. Hönig, Florian Flachsenberg, Christiane Ehrt, Alexander Neumann, Robert Schmidt, Christian Lemmen, Matthias Rarey
SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. J. Comput. Aided Mol. Des. 38 (1) (2024)
Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey
Redocking the PDB. J. Chem. Inf. Model. 64 (1) (2024)
Justin Lübbers, Uta F. Lessel, Matthias Rarey
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. J. Chem. Inf. Model. 64 (6) (2024)
Konrad Diedrich, Bennet Krause, Ole Berg, Matthias Rarey
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. J. Comput. Aided Mol. Des. 37 (10) (2023)
Torben Gutermuth, Jochen Sieg, Tim Stohn, Matthias Rarey
Modeling with Alternate Locations in X-ray Protein Structures. J. Chem. Inf. Model. 63 (8) (2023)
Joel Graef, Christiane Ehrt, Matthias Rarey
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. J. Chem. Inf. Model. 63 (10) (2023)
Martin Poppinga, Joel Graef, Konrad Diedrich, Matthias Rarey, Norbert Ritter
Database and Workflow Optimizations for Spatial-Geometric Queries in GeoMine. LWDA (2023)
Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona Hunter, Johannes Kirchmair, Karina Martínez-Mayorga, José L. Medina-Franco, Matthias Rarey, Alexander Tropsha, Alexandre Varnek, Barbara Zdrazil
School of cheminformatics in Latin America. J. Cheminformatics 15 (1) (2023)
Christian Meyenburg, Uschi Dolfus, Hans Briem, Matthias Rarey
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores. J. Comput. Aided Mol. Des. 37 (1) (2023)
Uschi Dolfus, Hans Briem, Torben Gutermuth, Matthias Rarey
Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures. J. Chem. Inf. Model. 63 (21) (2023)
Louis Bellmann, Raphael Klein, Matthias Rarey
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces. J. Chem. Inf. Model. 62 (11) (2022)
Patrick Penner, Virginie Y. Martiny, Louis Bellmann, Florian Flachsenberg, Marcus Gastreich, Isabelle Theret, Christophe Meyer, Matthias Rarey
FastGrow: on-the-fly growing and its application to DYRK1A. J. Comput. Aided Mol. Des. 36 (9) (2022)
Uschi Dolfus, Hans Briem, Matthias Rarey
Synthesis-Aware Generation of Structural Analogues. J. Chem. Inf. Model. 62 (15) (2022)
Uschi Dolfus, Hans Briem, Matthias Rarey
Visualizing Generic Reaction Patterns. J. Chem. Inf. Model. 62 (19) (2022)
Louis Bellmann, Patrick Penner, Marcus Gastreich, Matthias Rarey
Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. J. Chem. Inf. Model. 62 (3) (2022)
Wendy A. Warr, Marc C. Nicklaus, Christos A. Nicolaou, Matthias Rarey
Exploration of Ultralarge Compound Collections for Drug Discovery. J. Chem. Inf. Model. 62 (9) (2022)
Matthias Rarey, Marc C. Nicklaus, Wendy Warr
Special Issue on Reaction Informatics and Chemical Space. J. Chem. Inf. Model. 62 (9) (2022)
Katrin Schöning-Stierand, Konrad Diedrich, Christiane Ehrt, Florian Flachsenberg, Joel Graef, Jochen Sieg, Patrick Penner, Martin Poppinga, Annett Ungethüm, Matthias Rarey
: a comprehensive collection of web-based molecular modeling tools. Nucleic Acids Res. 50 (W1) (2022)
Tobias Harren, Hans Matter, Gerhard Hessler, Matthias Rarey, Christoph Grebner
Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence. J. Chem. Inf. Model. 62 (3) (2022)
Robert Schmidt, Raphael Klein, Matthias Rarey
Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. J. Chem. Inf. Model. 62 (9) (2022)
Patrick Penner, Wolfgang Guba, Robert Schmidt, Agnes Meyder, Martin Stahl, Matthias Rarey
The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. J. Chem. Inf. Model. 62 (7) (2022)
Konrad Diedrich, Joel Graef, Katrin Schöning-Stierand, Matthias Rarey
GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank. Bioinform. 37 (3) (2021)
Matthias Rarey, Marc C. Nicklaus, Wendy Warr
Call for Papers for the Special Issue: From Reaction Informatics to Chemical Space. J. Chem. Inf. Model. 61 (4) (2021)
Robert Schmidt, Florian Krull, Anna Lina Heinzke, Matthias Rarey
Disconnected Maximum Common Substructures under Constraints. J. Chem. Inf. Model. 61 (1) (2021)
Louis Bellmann, Patrick Penner, Matthias Rarey
Topological Similarity Search in Large Combinatorial Fragment Spaces. J. Chem. Inf. Model. 61 (1) (2021)
Florian Flachsenberg, Matthias Rarey
LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. J. Comput. Chem. 42 (15) (2021)
Patrick Penner, Virginie Y. Martiny, Arnaud Gohier, Marcus Gastreich, Pierre Ducrot, David Brown, Matthias Rarey
Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. J. Chem. Inf. Model. 60 (12) (2020)
Florian Flachsenberg, Agnes Meyder, Kai Sommer, Patrick Penner, Matthias Rarey
A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. J. Chem. Inf. Model. 60 (12) (2020)
Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. 60 (12) (2020)
Katrin Schöning-Stierand, Konrad Diedrich, Rainer Fährrolfes, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Ruben Steinegger, Matthias Rarey
: interactive analysis of protein-ligand binding interfaces. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Louis Bellmann, Patrick Penner, Matthias Rarey
Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration. J. Chem. Inf. Model. 59 (11) (2019)
Jochen Sieg, Florian Flachsenberg, Matthias Rarey
In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. J. Chem. Inf. Model. 59 (3) (2019)
Agnes Meyder, Stefanie Kampen, Jochen Sieg, Rainer Fährrolfes, Nils-Ole Friedrich, Florian Flachsenberg, Matthias Rarey
StructureProfiler: an all-in-one tool for 3D protein structure profiling. Bioinform. 35 (5) (2019)
Emanuel S. R. Ehmki, Robert Schmidt, Farina Ohm, Matthias Rarey
Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis. J. Chem. Inf. Model. 59 (6) (2019)
Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey
Conformator: A Novel Method for the Generation of Conformer Ensembles. J. Chem. Inf. Model. 59 (2) (2019)
Günter Klambauer, Sepp Hochreiter, Matthias Rarey
Machine Learning in Drug Discovery. J. Chem. Inf. Model. 59 (3) (2019)
Robert Schmidt, Emanuel S. R. Ehmki, Farina Ohm, Hans-Christian Ehrlich, Andriy Mashychev, Matthias Rarey
Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms. J. Chem. Inf. Model. 59 (6) (2019)
Sepp Hochreiter, Günter Klambauer, Matthias Rarey
Machine Learning in Drug Discovery. J. Chem. Inf. Model. 58 (9) (2018)
Eva Nittinger, Florian Flachsenberg, Stefan Bietz, Gudrun Lange, Robert Klein, Matthias Rarey
Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. J. Chem. Inf. Model. 58 (8) (2018)
Nils-Ole Friedrich, Christina de Bruyn Kops, Florian Flachsenberg, Kai Sommer, Matthias Rarey, Johannes Kirchmair
Benchmarking Commercial Conformer Ensemble Generators. J. Chem. Inf. Model. 57 (11) (2017)
Agnes Meyder, Eva Nittinger, Gudrun Lange, Robert Klein, Matthias Rarey
Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. J. Chem. Inf. Model. 57 (10) (2017)
Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey
ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res. 45 (Webserver-Issue) (2017)
Mathias M. von Behren, Matthias Rarey
Ligand-based virtual screening under partial shape constraints. J. Comput. Aided Mol. Des. 31 (4) (2017)
Therese Inhester, Eva Nittinger, Kai Sommer, Pascal Schmidt, Stefan Bietz, Matthias Rarey
nova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures. J. Chem. Inf. Model. 57 (9) (2017)
Florian Flachsenberg, Niek Andresen, Matthias Rarey
RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. J. Chem. Inf. Model. 57 (2) (2017)
Therese Inhester, Stefan Bietz, Matthias Hilbig, Robert Schmidt, Matthias Rarey
Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces. J. Chem. Inf. Model. 57 (2) (2017)
Nils-Ole Friedrich, Agnes Meyder, Christina de Bruyn Kops, Kai Sommer, Florian Flachsenberg, Matthias Rarey, Johannes Kirchmair
High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. J. Chem. Inf. Model. 57 (3) (2017)
Wolfgang Guba, Agnes Meyder, Matthias Rarey, Jérôme Hert
Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules. J. Chem. Inf. Model. 56 (1) (2016)
Stefan Bietz, Matthias Rarey
SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. J. Chem. Inf. Model. 56 (1) (2016)
Tobias Lang, Florian Flachsenberg, Ulrike von Luxburg, Matthias Rarey
Feasibility of Active Machine Learning for Multiclass Compound Classification. J. Chem. Inf. Model. 56 (1) (2016)
Mathias M. von Behren, Stefan Bietz, Eva Nittinger, Matthias Rarey
mRAISE: an alternative algorithmic approach to ligand-based virtual screening. J. Comput. Aided Mol. Des. 30 (8) (2016)
Kai Sommer, Nils-Ole Friedrich, Stefan Bietz, Matthias Hilbig, Therese Inhester, Matthias Rarey
UNICON: A Powerful and Easy-to-Use Compound Library Converter. J. Chem. Inf. Model. 56 (6) (2016)
Florian Lauck, Matthias Rarey
FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption. J. Chem. Inf. Model. 56 (9) (2016)
Matthias Hilbig, Matthias Rarey
MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing. J. Chem. Inf. Model. 55 (10) (2015)
Markus Wagener, Frank Oellien, Uli Fechner, Matthias Rarey
10th ICCS/GCC Conference: 40 Years of Cheminformatics. J. Chem. Inf. Model. 55 (6) (2015)
Kenneth M. Merz Jr., Matthias Rarey, Alexander Tropsha, Habibah A. Wahab
Letter from the Editors. J. Chem. Inf. Model. 55 (4) (2015)
Stefan Bietz, Karen T. Schomburg, Matthias Hilbig, Matthias Rarey
Discriminative Chemical Patterns: Automatic and Interactive Design. J. Chem. Inf. Model. 55 (8) (2015)
Stefan Bietz, Matthias Rarey
ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. J. Chem. Inf. Model. 55 (8) (2015)
Eva Nittinger, Nadine Schneider, Gudrun Lange, Matthias Rarey
Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density. J. Chem. Inf. Model. 55 (4) (2015)
Sascha Urbaczek, Adrian Kolodzik, Matthias Rarey
The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States. J. Chem. Inf. Model. 54 (3) (2014)
Karen T. Schomburg, Matthias Rarey
Facing the challenges of computational target prediction. J. Cheminformatics 6 (S-1) (2014)
Eva Vennmann, Nadine Schneider, Gudrun Lange, Matthias Rarey
Elucidating protein-protein interactions using the HYDE scoring function. J. Cheminformatics 6 (S-1) (2014)
Karen Schomburg, Stefan Bietz, Hans Briem, Angela M. Henzler, Sascha Urbaczek, Matthias Rarey
Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening. J. Chem. Inf. Model. 54 (6) (2014)
Katrin Stierand, Tim Harder, Lothar Wissler, Christian Lemmen, Matthias Rarey
Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web. J. Cheminformatics 6 (S-1) (2014)
Stefan Bietz, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. J. Cheminformatics 6 (1) (2014)
Angela M. Henzler, Sascha Urbaczek, Matthias Hilbig, Matthias Rarey
An integrated approach to knowledge-driven structure-based virtual screening. J. Comput. Aided Mol. Des. 28 (9) (2014)
Karen Schomburg, Matthias Rarey
Benchmark Data Sets for Structure-Based Computational Target Prediction. J. Chem. Inf. Model. 54 (8) (2014)
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. J. Comput. Aided Mol. Des. 27 (1) (2013)
Matthias Rarey, Adrian Kolodzik, Sascha Urbaczek
Let's talk about rings. J. Cheminformatics 5 (S-1) (2013)
Matthias Wirth, Andrea Volkamer, Vincent Zoete, Friedrich Rippmann, Olivier Michielin, Matthias Rarey, Wolfgang H. B. Sauer
Protein pocket and ligand shape comparison and its application in virtual screening. J. Comput. Aided Mol. Des. 27 (6) (2013)
Hans-Christian Ehrlich, Angela M. Henzler, Matthias Rarey
Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces. J. Chem. Inf. Model. 53 (7) (2013)
Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey
TorsionAnalyzer: exploring conformational space. J. Cheminformatics 5 (S-1) (2013)
Sascha Urbaczek, Adrian Kolodzik, Inken Groth, Stefan Heuser, Matthias Rarey
Reading PDB: Perception of Molecules from 3D Atomic Coordinates. J. Chem. Inf. Model. 53 (1) (2013)
Matthias Hilbig, Sascha Urbaczek, Inken Groth, Stefan Heuser, Matthias Rarey
MONA - Interactive manipulation of molecule collections. J. Cheminformatics 5 (2013)
Mathias M. von Behren, Andrea Volkamer, Angela M. Henzler, Karen Schomburg, Sascha Urbaczek, Matthias Rarey
Fast Protein Binding Site Comparison via an Index-Based Screening Technology. J. Chem. Inf. Model. 53 (2) (2013)
Lennart Heinzerling, Matthias Rarey
Force-field-based minimizations of protein-ligand complexes in the blink of an eye. J. Cheminformatics 5 (S-1) (2013)
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. J. Comput. Aided Mol. Des. 26 (6) (2012)
Andrea Volkamer, Daniel Kuhn, Thomas Grombacher, Friedrich Rippmann, Matthias Rarey
Combining Global and Local Measures for Structure-Based Druggability Predictions. J. Chem. Inf. Model. 52 (2) (2012)
Hans-Christian Ehrlich, Matthias Rarey
Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2. J. Cheminformatics 4 (2012)
Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey
Systematic search for pairwise dependencies of torsion angles. J. Cheminformatics 4 (S-1) (2012)
Tanja Schulz-Gasch, Christin Schärfer, Wolfgang Guba, Matthias Rarey
TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. J. Chem. Inf. Model. 52 (6) (2012)
Matthias Rarey
Some thoughts on the "A" in computer-aided molecular design. J. Comput. Aided Mol. Des. 26 (1) (2012)
Uta F. Lessel, Bernd Wellenzohn, J. Robert Fischer, Matthias Rarey
Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT. J. Chem. Inf. Model. 52 (2) (2012)
Adrian Kolodzik, Sascha Urbaczek, Matthias Rarey
Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies. J. Chem. Inf. Model. 52 (8) (2012)
Andrea Volkamer, Daniel Kuhn, Friedrich Rippmann, Matthias Rarey
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinform. 28 (15) (2012)
Hans-Christian Ehrlich, Andrea Volkamer, Matthias Rarey
Searching for Substructures in Fragment Spaces. J. Chem. Inf. Model. 52 (12) (2012)
Angela M. Henzler, Sascha Urbaczek, Benjamin Schulz, Matthias Rarey
A flexible-hydrogen interaction model for protein-ligand docking. J. Cheminformatics 4 (S-1) (2012)
Lennart Heinzerling, Robert Klein, Matthias Rarey
Fast force field-based optimization of protein-ligand complexes with graphics processor. J. Comput. Chem. 33 (32) (2012)
Matthias Hilbig, Matthias Rarey
Aligning chemical structure diagrams with local search. J. Cheminformatics 4 (S-1) (2012)
Karen Schomburg, Hans-Christian Ehrlich, Katrin Stierand, Matthias Rarey
Chemical pattern visualization in 2D - the SMARTSviewer. J. Cheminformatics 3 (S-1) (2011)
Sascha Urbaczek, Adrian Kolodzik, J. Robert Fischer, Tobias Lippert, Stefan Heuser, Inken Groth, Tanja Schulz-Gasch, Matthias Rarey
NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats. J. Chem. Inf. Model. 51 (12) (2011)
Nadine Schneider, Gudrun Lange, Robert Klein, Christian Lemmen, Matthias Rarey
HYDEing the false positives - scoring for lead optimization. J. Cheminformatics 3 (S-1) (2011)
J. Robert Fischer, Uta F. Lessel, Matthias Rarey
Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees. J. Chem. Inf. Model. 51 (9) (2011)
Hans-Christian Ehrlich, Matthias Rarey
Searching substructures in fragment spaces. J. Cheminformatics 3 (S-1) (2011)
Stefan Bietz, Sascha Urbaczek, Matthias Rarey
Hydrogen placement in protein-ligand complexes under consideration of tautomerism. J. Cheminformatics 3 (S-1) (2011)
Katrin Stierand, Matthias Rarey
Consistent two-dimensional visualization of protein-ligand complex series. J. Cheminformatics 3 (2011)
Tobias Lippert, Tanja Schulz-Gasch, Olivier Roche, Wolfgang Guba, Matthias Rarey
De novo design by pharmacophore-based searches in fragment spaces. J. Comput. Aided Mol. Des. 25 (10) (2011)
Katrin Stierand, Matthias Rarey
PoseView - molecular interaction patterns at a glance. J. Cheminformatics 2 (S-1) (2010)

Matthias Rarey.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Matthias Rarey