Matthias Rarey

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 70

Top Topics

Molecular Docking

Top Venues

Journal of chemical information and modeling

Journal of computer-aided molecular design

Journal of medicinal chemistry

This page only lists publications with an associated author ORCID identifier.

Publications

Konrad Diedrich, Christiane Ehrt, Joel Graef, Martin Poppinga, Norbert Ritter, Matthias Rarey
User-centric design of a 3D search interface for protein-ligand complexes. Journal of computer-aided molecular design 38 (1) (2024)
Justin Lübbers, Uta Lessel, Matthias Rarey
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. Journal of chemical information and modeling 64 (6) (2024)
Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. Journal of chemical information and modeling 64 (8) (2024)
Justin Lübbers, Uta Lessel, Matthias Rarey
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. Journal of chemical information and modeling 64 (6) (2024)
Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. Journal of chemical information and modeling 64 (8) (2024)
Thorben Reim, Christiane Ehrt, Joel Graef, Sebastian Günther, Alke Meents, Matthias Rarey
SiteMine: Large-scale binding site similarity searching in protein structure databases. Archiv der Pharmazie 357 (5) (2024)
Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. Journal of chemical information and modeling 64 (8) (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. Journal of computer-aided molecular design 38 (1) (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. Journal of computer-aided molecular design 38 (1) (2024)
Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. Journal of chemical information and modeling (2024)
Justin Lübbers, Uta Lessel, Matthias Rarey
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. Journal of chemical information and modeling 64 (6) (2024)
Justin Lübbers, Uta Lessel, Matthias Rarey
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. Journal of chemical information and modeling 64 (6) (2024)
Justin Lübbers, Uta Lessel, Matthias Rarey
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. Journal of chemical information and modeling (2024)
Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. Journal of chemical information and modeling 64 (8) (2024)
Justin Lübbers, Uta Lessel, Matthias Rarey
Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. Journal of chemical information and modeling 64 (6) (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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 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. Journal of computer-aided molecular design 38 (1) (2024)
Joel Graef, Christiane Ehrt, Thorben Reim, Matthias Rarey
Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. Journal of chemical information and modeling 64 (8) (2024)
Thorben Reim, Christiane Ehrt, Joel Graef, Sebastian Günther, Alke Meents, Matthias Rarey
SiteMine: Large-scale binding site similarity searching in protein structure databases. Archiv der Pharmazie (2024)
Jochen Sieg, Matthias Rarey
Searching similar local 3D micro-environments in protein structure databases with MicroMiner. Briefings in bioinformatics 24 (6) (2023)
Joel Graef, Christiane Ehrt, Matthias Rarey
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) (2023)
Joel Graef, Christiane Ehrt, Matthias Rarey
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) (2023)
Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey
Redocking the PDB. Journal of chemical information and modeling 64 (1) (2023)
Konrad Diedrich, Bennet Krause, Ole Berg, Matthias Rarey
PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. Journal of computer-aided molecular design (2023)
Uschi Dolfus, Hans Briem, Torben Gutermuth, Matthias Rarey
Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures. Journal of chemical information and modeling (2023)
Torben Gutermuth, Jochen Sieg, Tim Stohn, Matthias Rarey
Modeling with Alternate Locations in X-ray Protein Structures. Journal of chemical information and modeling (2023)
Joel Graef, Christiane Ehrt, Matthias Rarey
Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. Journal of chemical information and modeling (2023)
Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey
Redocking the PDB. Journal of chemical information and modeling 64 (1) (2023)
Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey
Redocking the PDB. Journal of chemical information and modeling 64 (1) (2023)
Florian Flachsenberg, Christiane Ehrt, Torben Gutermuth, Matthias Rarey
Redocking the PDB. Journal of chemical information and modeling (2023)
Louis Bellmann, Raphael Klein, Matthias Rarey
Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces. Journal of chemical information and modeling 62 (11) (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. Journal of chemical information and modeling 62 (3) (2022)
Patrick Penner, Wolfgang Guba, Robert Schmidt, Agnes Meyder, Martin Stahl, Matthias Rarey
The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. Journal of chemical information and modeling 62 (7) (2022)
Christian Meyenburg, Uschi Dolfus, Hans Briem, Matthias Rarey
Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores. Journal of computer-aided molecular design (2022)
Uschi Dolfus, Hans Briem, Matthias Rarey
Synthesis-Aware Generation of Structural Analogues. Journal of chemical information and modeling 62 (15) (2022)
Katrin Schöning-Stierand, Konrad Diedrich, Christiane Ehrt, Florian Flachsenberg, Joel Graef, Jochen Sieg, Patrick Penner, Martin Poppinga, Annett Ungethüm, Matthias Rarey
ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. Nucleic acids research (2022)
Louis Bellmann, Patrick Penner, Marcus Gastreich, Matthias Rarey
Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. Journal of chemical information and modeling 62 (3) (2022)
Uschi Dolfus, Hans Briem, Matthias Rarey
Visualizing Generic Reaction Patterns. Journal of chemical information and modeling 62 (19) (2022)
Wendy A Warr, Marc C Nicklaus, Christos A Nicolaou, Matthias Rarey
Exploration of Ultralarge Compound Collections for Drug Discovery. Journal of chemical information and modeling 62 (9) (2022)
Matthias Rarey, Marc C Nicklaus, Wendy A Warr
Special Issue on Reaction Informatics and Chemical Space. Journal of chemical information and modeling 62 (9) (2022)
Patrick Penner, Virginie Martiny, Louis Bellmann, Florian Flachsenberg, Marcus Gastreich, Isabelle Theret, Christophe Meyer, Matthias Rarey
FastGrow: on-the-fly growing and its application to DYRK1A. Journal of computer-aided molecular design 36 (9) (2022)
Robert Schmidt, Raphael Klein, Matthias Rarey
Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. Journal of chemical information and modeling (2021)
Florian Flachsenberg, Matthias Rarey
LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. Journal of computational chemistry 42 (15) (2021)
Kenneth M Merz, Rommie Elizabeth Amaro, Zoe Cournia, Matthias Rarey, Thereza A Soares, Alexander Trospsha, Habibah Abdul Wahab, Ren-Xiao Wang
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. Journal of chemical information and modeling 60 (12) (2021)
Joel Graef, Christiane Ehrt, Konrad Diedrich, Martin Poppinga, Norbert Ritter, Matthias Rarey
Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures. Journal of medicinal chemistry (2021)
Sebastian Günther, Patrick Y A Reinke, Yaiza Fernández-García, Julia Lieske, Thomas J Lane, Helen Mary Ginn, Faisal H M Koua, Christiane Ehrt, Wiebke Ewert, Dominik Oberthür, Oleksandr Yefanov, Susanne Meier, Kristina Lorenzen, Boris Krichel, Janine-Denise Kopicki, Luca Gelisio, Wolfgang Brehm, Ilona Dunkel, Brandon Seychell, Henry Gieseler, Brenna Norton-Baker, Beatriz Escudero-Pérez, Martin Domaracky, Sofiane Saouane, Alexandra Tolstikova, Thomas A White, Anna Hänle, Michael Groessler, Holger Fleckenstein, Fabian Trost, Marina Galchenkova, Yaroslav Gevorkov, Chufeng Li, Salah Awel, Ariana Peck, Miriam Barthelmess, Frank Schlünzen, Paul Lourdu Xavier, Nadine Werner, Hina Andaleeb, Najeeb Ullah, Sven Falke, Vasundara Srinivasan, Bruno Alves França, Martin Schwinzer, Hévila Brognaro, Cromarte Rogers, Diogo Melo, Joanna J Zaitseva-Doyle, Juraj Knoška, Gisel Esperanza Pena Murillo, Aida Rahmani Mashhour, Vincent Hennicke, Pontus Fischer, Johanna Hakanpää, Jan Meyer, Philip Gribbon, Bernhard Ellinger, Maria Kuzikov, Markus Wolf, Andrea Rosario Beccari, Gleb Bourenkov, David von Stetten, Guillaume Pompidor, Isabel Bento, Saravanan Panneerselvam, Ivars Karpics, Thomas R Schneider, Maria Marta Garcia-Alai, Stephan Niebling, Christian Günther, Christina Schmidt, Robin Schubert, Huijong Han, Juliane Boger, Diana C F Monteiro, Linlin Zhang, Xinyuanyuan Sun, Jonathan Pletzer-Zelgert, Jan Wollenhaupt, Christian G Feiler, Manfred S Weiss, Eike-Christian Schulz, Pedram Mehrabi, Katarina Karničar, Aleksandra Usenik, Jure Loboda, Henning Tidow, Ashwin Chari, Rolf Hilgenfeld, Charlotte Uetrecht, Russell J Cox, Andrea Zaliani, Tobias Beck, Matthias Rarey, Stephan Gunther, Dusan Turk, Winfried Hinrichs, Henry N Chapman, Arwen R Pearson, Christian Betzel, Alke Meents
X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science (New York, N.Y.) 372 (6542) (2021)
Guenter Klambauer, Sepp Hochreiter, Matthias Rarey
Machine Learning in Drug Discovery. Journal of chemical information and modeling 59 (3) (2020)
Louis Bellmann, Patrick Penner, Matthias Rarey
Topological Similarity Search in Large Combinatorial Fragment Spaces. Journal of chemical information and modeling 61 (1) (2020)
Christiane Ehrt, Bennet Krause, Robert Schmidt, Emanuel S R Ehmki, Matthias Rarey
SMARTS.plus - A Toolbox for Chemical Pattern Design. Molecular informatics 39 (12) (2020)
Robert Schmidt, Florian Krull, Anna Lina Heinzke, Matthias Rarey
Disconnected Maximum Common Substructures under Constraints. Journal of chemical information and modeling 61 (1) (2020)
Florian Flachsenberg, Agnes Meyder, Kai Sommer, Patrick Penner, Matthias Rarey
A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. Journal of chemical information and modeling 60 (12) (2020)
Patrick Penner, Virginie Martiny, Arnaud Gohier, Marcus Gastreich, Pierre Ducrot, David Brown, Matthias Rarey
Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. Journal of chemical information and modeling 60 (12) (2020)
Emanuel S R Ehmki, Robert Schmidt, Farina Ohm, Matthias Rarey
Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis. Journal of chemical information and modeling 59 (6) (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. Journal of chemical information and modeling 59 (6) (2019)
Jochen Sieg, Florian Flachsenberg, Matthias Rarey
In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. Journal of chemical information and modeling 59 (3) (2019)
Louis Bellmann, Patrick Penner, Matthias Rarey
Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration. Journal of chemical information and modeling 59 (11) (2019)
Nils-Ole Friedrich, Florian Flachsenberg, Agnes Meyder, Kai Sommer, Johannes Kirchmair, Matthias Rarey
Conformator: A Novel Method for the Generation of Conformer Ensembles. Journal of chemical information and modeling 59 (2) (2019)
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. Journal of chemical information and modeling 58 (8) (2018)
Emanuel S R Ehmki, Matthias Rarey
Exploring Structure-Activity Relationships with Three-Dimensional Matched Molecular Pairs-A Review. ChemMedChem 13 (6) (2018)
Sepp Hochreiter, Guenter Klambauer, Matthias Rarey
Machine Learning in Drug Discovery. Journal of chemical information and modeling 58 (9) (2018)
Nils-Ole Friedrich, Christina de Bruyn Kops, Florian Flachsenberg, Kai Sommer, Matthias Rarey, Johannes Kirchmair
Benchmarking Commercial Conformer Ensemble Generators. Journal of chemical information and modeling 57 (11) (2017)
Therese Inhester, Stefan Bietz, Matthias Hilbig, Robert Schmidt, Matthias Rarey
Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces. Journal of chemical information and modeling 57 (2) (2017)
Florian Flachsenberg, Niek Andresen, Matthias Rarey
RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. Journal of chemical information and modeling 57 (2) (2017)
Vincent Wagner, Linda Jantz, Hans Briem, Kai Sommer, Matthias Rarey, Clara D Christ
Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation. ChemMedChem 12 (22) (2017)
Eva Nittinger, Therese Inhester, Stefan Bietz, Agnes Meyder, Karen T Schomburg, Gudrun Lange, Robert Klein, Matthias Rarey
Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces. Journal of medicinal chemistry 60 (10) (2017)
Karen T Schomburg, Eva Nittinger, Agnes Meyder, Stefan Bietz, Nadine Schneider, Gudrun Lange, Robert Klein, Matthias Rarey
Prediction of protein mutation effects based on dehydration and hydrogen bonding - A large-scale study. Proteins 85 (8) (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. Journal of chemical information and modeling 57 (10) (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. Journal of chemical information and modeling 57 (3) (2017)
Therese Inhester, Eva Nittinger, Kai Sommer, Pascal Schmidt, Stefan Bietz, Matthias Rarey
NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures. Journal of chemical information and modeling 57 (9) (2017)