Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins. - Matthias Rarey; Bernd Kramer; Thomas Lengauer (ISMB, 1995)

Rechnergestützte Vorhersage von Rezeptor-Ligand-Wechselwirkungen. - Matthias Rarey (Oldenbourg, 1996)

Placement of medium-sized molecular fragments into active sites of proteins. - Matthias Rarey; Stephan Wefing; Thomas Lengauer (J. Comput. Aided Mol. Des., 1996)

Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. - Matthias Rarey; Bernd Kramer; Thomas Lengauer (J. Comput. Aided Mol. Des., 1997)

Feature trees: A new molecular similarity measure based on tree matching. - Matthias Rarey; J. Scott Dixon (J. Comput. Aided Mol. Des., 1998)

Docking of hydrophobic ligands with interaction-based matching algorithms. - Matthias Rarey; Bernd Kramer; Thomas Lengauer (Bioinform., 1999)

Algorithmen für den computergestützten Wirkstoffentwurf. - Matthias Rarey (GMD, 2001)

Similarity searching in large combinatorial chemistry spaces. - Matthias Rarey; Martin Stahl (J. Comput. Aided Mol. Des., 2001)

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

Flexible docking under pharmacophore type constraints. - Sally A. Hindle; Matthias Rarey; Christian Buning; Thomas Lengauer (J. Comput. Aided Mol. Des., 2002)

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources. - Torsten Crass; Iris Antes; Rico Basekow; Peer Bork; Christian Buning; Maik Christensen; Holger Claussen 002; Christian Ebeling; Peter Ernst; Valérie Gailus-Durner; Karl-Heinz Glatting; Rolf Gohla; et al. (Bioinform., 2004)

Automated Drawing of Structural Molecular Formulas under Constraints. - Patrick C. Fricker; Marcus Gastreich; Matthias Rarey (J. Chem. Inf. Model., 2004)

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

Molecular complexes at a glance: automated generation of two-dimensional complex diagrams. - Katrin Stierand; Patrick C. Maaß; Matthias Rarey (Bioinform., 2006)

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. - Andreas Kämper; Joannis Apostolakis; Matthias Rarey; Christel M. Marian; Thomas Lengauer (J. Chem. Inf. Model., 2006)

Exploring fragment spaces under multiple physicochemical constraints. - Juri Pärn; Jörg Degen; Matthias Rarey (J. Comput. Aided Mol. Des., 2007)

TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. - Ingo Schellhammer; Matthias Rarey (J. Comput. Aided Mol. Des., 2007)

SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering. - J. Robert Fischer; Matthias Rarey (J. Chem. Inf. Model., 2007)

Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations. - Patrick C. Maaß; Tanja Schulz-Gasch; Martin Stahl; Matthias Rarey (J. Chem. Inf. Model., 2007)

Second-generation de novo design: a view from a medicinal chemist perspective. - Andrea Zaliani; Krisztina Boda; Thomas Seidel; Achim Herwig; Christof H. Schwab; Johann Gasteiger; Holger Claussen 002; Christian Lemmen; Jörg Degen; Juri Pärn; Matthias Rarey (J. Comput. Aided Mol. Des., 2009)

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

Conformational Sampling for Large-Scale Virtual Screening: Accuracy versus Ensemble Size. - Axel Griewel; Ole Kayser; Jochen Schlosser; Matthias Rarey (J. Chem. Inf. Model., 2009)

Beyond the Virtual Screening Paradigm: Structure-Based Searching for New Lead Compounds. - Jochen Schlosser; Matthias Rarey (J. Chem. Inf. Model., 2009)

PoseView - molecular interaction patterns at a glance. - Katrin Stierand; Matthias Rarey (J. Cheminformatics, 2010)

Where are the boundaries? Automated pocket detection for druggability studies. - Andrea Volkamer; Thomas Grombacher; Matthias Rarey (J. Cheminformatics, 2010)

LoFT: Similarity-Driven Multiobjective Focused Library Design. - J. Robert Fischer; Uta F. Lessel; Matthias Rarey (J. Chem. Inf. Model., 2010)

From Structure Diagrams to Visual Chemical Patterns. - Karen Schomburg; Hans-Christian Ehrlich; Katrin Stierand; Matthias Rarey (J. Chem. Inf. Model., 2010)

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. - Andrea Volkamer; Axel Griewel; Thomas Grombacher; Matthias Rarey (J. Chem. Inf. Model., 2010)

De novo design by pharmacophore-based searches in fragment spaces. - Tobias Lippert; Tanja Schulz-Gasch; Olivier Roche; Wolfgang Guba; Matthias Rarey (J. Comput. Aided Mol. Des., 2011)

Hydrogen placement in protein-ligand complexes under consideration of tautomerism. - Stefan Bietz; Sascha Urbaczek; Matthias Rarey (J. Cheminformatics, 2011)

Searching substructures in fragment spaces. - Hans-Christian Ehrlich; Matthias Rarey (J. Cheminformatics, 2011)

HYDEing the false positives - scoring for lead optimization. - Nadine Schneider; Gudrun Lange; Robert Klein; Christian Lemmen; Matthias Rarey (J. Cheminformatics, 2011)

Chemical pattern visualization in 2D - the SMARTSviewer. - Karen Schomburg; Hans-Christian Ehrlich; Katrin Stierand; Matthias Rarey (J. Cheminformatics, 2011)

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

Improving Similarity-Driven Library Design: Customized Matching and Regioselective Feature Trees. - J. Robert Fischer; Uta F. Lessel; Matthias Rarey (J. Chem. Inf. Model., 2011)

NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats. - Sascha Urbaczek; Adrian Kolodzik; J. Robert Fischer; Tobias Lippert; Stefan Heuser; Inken Groth; Tanja Schulz-Gasch; Matthias Rarey (J. Chem. Inf. Model., 2011)

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

Some thoughts on the "A" in computer-aided molecular design. - Matthias Rarey (J. Comput. Aided Mol. Des., 2012)

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function. - Nadine Schneider; Sally A. Hindle; Gudrun Lange; Robert Klein; Jürgen Albrecht; Hans Briem; Kristin Beyer; Holger Claußen 002; Marcus Gastreich; Christian Lemmen; Matthias Rarey (J. Comput. Aided Mol. Des., 2012)

Fast force field-based optimization of protein-ligand complexes with graphics processor. - Lennart Heinzerling; Robert Klein; Matthias Rarey (J. Comput. Chem., 2012)

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

A flexible-hydrogen interaction model for protein-ligand docking. - Angela M. Henzler; Sascha Urbaczek; Benjamin Schulz; Matthias Rarey (J. Cheminformatics, 2012)

Aligning chemical structure diagrams with local search. - Matthias Hilbig 001; Matthias Rarey (J. Cheminformatics, 2012)

Systematic search for pairwise dependencies of torsion angles. - Christin Schärfer; Tanja Schulz-Gasch; Matthias Rarey (J. Cheminformatics, 2012)

Searching for Substructures in Fragment Spaces. - Hans-Christian Ehrlich; Andrea Volkamer; Matthias Rarey (J. Chem. Inf. Model., 2012)

Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies. - Adrian Kolodzik; Sascha Urbaczek; Matthias Rarey (J. Chem. Inf. Model., 2012)

Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT. - Uta F. Lessel; Bernd Wellenzohn; J. Robert Fischer; Matthias Rarey (J. Chem. Inf. Model., 2012)

TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations. - Tanja Schulz-Gasch; Christin Schärfer; Wolfgang Guba; Matthias Rarey (J. Chem. Inf. Model., 2012)

Combining Global and Local Measures for Structure-Based Druggability Predictions. - Andrea Volkamer; Daniel Kuhn; Thomas Grombacher; Friedrich Rippmann; Matthias Rarey (J. Chem. Inf. Model., 2012)

A consistent description of HYdrogen bond and DEhydration energies in protein-ligand complexes: methods behind the HYDE scoring function. - Nadine Schneider; Gudrun Lange; Sally A. Hindle; Robert Klein; Matthias Rarey (J. Comput. Aided Mol. Des., 2013)

Protein pocket and ligand shape comparison and its application in virtual screening. - Matthias Wirth; Andrea Volkamer; Vincent Zoete; Friedrich Rippmann; Olivier Michielin; Matthias Rarey; Wolfgang H. B. Sauer (J. Comput. Aided Mol. Des., 2013)

Force-field-based minimizations of protein-ligand complexes in the blink of an eye. - Lennart Heinzerling; Matthias Rarey (J. Cheminformatics, 2013)

MONA - Interactive manipulation of molecule collections. - Matthias Hilbig 001; Sascha Urbaczek; Inken Groth; Stefan Heuser; Matthias Rarey (J. Cheminformatics, 2013)

Let's talk about rings. - Matthias Rarey; Adrian Kolodzik; Sascha Urbaczek (J. Cheminformatics, 2013)

TorsionAnalyzer: exploring conformational space. - Christin Schärfer; Tanja Schulz-Gasch; Matthias Rarey (J. Cheminformatics, 2013)

Fast Protein Binding Site Comparison via an Index-Based Screening Technology. - Mathias M. von Behren; Andrea Volkamer; Angela M. Henzler; Karen Schomburg; Sascha Urbaczek; Matthias Rarey (J. Chem. Inf. Model., 2013)

Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces. - Hans-Christian Ehrlich; Angela M. Henzler; Matthias Rarey (J. Chem. Inf. Model., 2013)

Reading PDB: Perception of Molecules from 3D Atomic Coordinates. - Sascha Urbaczek; Adrian Kolodzik; Inken Groth; Stefan Heuser; Matthias Rarey (J. Chem. Inf. Model., 2013)

An integrated approach to knowledge-driven structure-based virtual screening. - Angela M. Henzler; Sascha Urbaczek; Matthias Hilbig 001; Matthias Rarey (J. Comput. Aided Mol. Des., 2014)

Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. - Stefan Bietz; Sascha Urbaczek; Benjamin Schulz; Matthias Rarey (J. Cheminformatics, 2014)

Facing the challenges of computational target prediction. - Karen T. Schomburg; Matthias Rarey (J. Cheminformatics, 2014)

Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web. - Katrin Stierand; Tim Harder; Lothar Wissler; Christian Lemmen; Matthias Rarey (J. Cheminformatics, 2014)

Elucidating protein-protein interactions using the HYDE scoring function. - Eva Vennmann; Nadine Schneider; Gudrun Lange; Matthias Rarey (J. Cheminformatics, 2014)

Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening. - Karen Schomburg; Stefan Bietz; Hans Briem; Angela M. Henzler; Sascha Urbaczek; Matthias Rarey (J. Chem. Inf. Model., 2014)

Benchmark Data Sets for Structure-Based Computational Target Prediction. - Karen Schomburg; Matthias Rarey (J. Chem. Inf. Model., 2014)

The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States. - Sascha Urbaczek; Adrian Kolodzik; Matthias Rarey (J. Chem. Inf. Model., 2014)

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. - Stefan Bietz; Matthias Rarey (J. Chem. Inf. Model., 2015)

Discriminative Chemical Patterns: Automatic and Interactive Design. - Stefan Bietz; Karen T. Schomburg; Matthias Hilbig 001; Matthias Rarey (J. Chem. Inf. Model., 2015)

MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing. - Matthias Hilbig 001; Matthias Rarey (J. Chem. Inf. Model., 2015)

Letter from the Editors. - Kenneth M. Merz Jr.; Matthias Rarey; Alexander Tropsha; Habibah A. Wahab (J. Chem. Inf. Model., 2015)

Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density. - Eva Nittinger; Nadine Schneider; Gudrun Lange; Matthias Rarey (J. Chem. Inf. Model., 2015)

10th ICCS/GCC Conference: 40 Years of Cheminformatics. - Markus Wagener; Frank Oellien; Uli Fechner; Matthias Rarey (J. Chem. Inf. Model., 2015)

mRAISE: an alternative algorithmic approach to ligand-based virtual screening. - Mathias M. von Behren; Stefan Bietz; Eva Nittinger; Matthias Rarey (J. Comput. Aided Mol. Des., 2016)

SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles. - Stefan Bietz; Matthias Rarey (J. Chem. Inf. Model., 2016)

Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules. - Wolfgang Guba; Agnes Meyder; Matthias Rarey; Jérôme Hert (J. Chem. Inf. Model., 2016)

Feasibility of Active Machine Learning for Multiclass Compound Classification. - Tobias Lang 001; Florian Flachsenberg; Ulrike von Luxburg; Matthias Rarey (J. Chem. Inf. Model., 2016)

FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption. - Florian Lauck; Matthias Rarey (J. Chem. Inf. Model., 2016)

UNICON: A Powerful and Easy-to-Use Compound Library Converter. - Kai Sommer; Nils-Ole Friedrich; Stefan Bietz; Matthias Hilbig 001; Therese Inhester; Matthias Rarey (J. Chem. Inf. Model., 2016)

Ligand-based virtual screening under partial shape constraints. - Mathias M. von Behren; Matthias Rarey (J. Comput. Aided Mol. Des., 2017)

RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. - Florian Flachsenberg; Niek Andresen; Matthias Rarey (J. Chem. Inf. Model., 2017)

High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. - Nils-Ole Friedrich; Agnes Meyder; Christina de Bruyn Kops; Kai Sommer; Florian Flachsenberg; Matthias Rarey; Johannes Kirchmair (J. Chem. Inf. Model., 2017)

Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces. - Therese Inhester; Stefan Bietz; Matthias Hilbig 001; Robert Schmidt 002; Matthias Rarey (J. Chem. Inf. Model., 2017)

ProteinsPlus: a web portal for structure analysis of macromolecules. - Rainer Fährrolfes; Stefan Bietz; Florian Flachsenberg; Agnes Meyder; Eva Nittinger; Thomas Otto; Andrea Volkamer; Matthias Rarey (Nucleic Acids Res., 2017)

NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures. - Therese Inhester; Eva Nittinger; Kai Sommer; Pascal Schmidt; Stefan Bietz; Matthias Rarey (J. Chem. Inf. Model., 2017)

Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. - Agnes Meyder; Eva Nittinger; Gudrun Lange; Robert Klein; Matthias Rarey (J. Chem. Inf. Model., 2017)

Benchmarking Commercial Conformer Ensemble Generators. - Nils-Ole Friedrich; Christina de Bruyn Kops; Florian Flachsenberg; Kai Sommer; Matthias Rarey; Johannes Kirchmair (J. Chem. Inf. Model., 2017)

Machine Learning in Drug Discovery. - Sepp Hochreiter; Günter Klambauer; Matthias Rarey (J. Chem. Inf. Model., 2018)

Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. - Eva Nittinger; Florian Flachsenberg; Stefan Bietz; Gudrun Lange; Robert Klein; Matthias Rarey (J. Chem. Inf. Model., 2018)

StructureProfiler: an all-in-one tool for 3D protein structure profiling. - Agnes Meyder; Stefanie Kampen; Jochen Sieg; Rainer Fährrolfes; Nils-Ole Friedrich; Florian Flachsenberg; Matthias Rarey (Bioinform., 2019)

Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration. - Louis Bellmann; Patrick Penner; Matthias Rarey (J. Chem. Inf. Model., 2019)

Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis. - Emanuel S. R. Ehmki; Robert Schmidt 002; Farina Ohm; Matthias Rarey (J. Chem. Inf. Model., 2019)

Conformator: A Novel Method for the Generation of Conformer Ensembles. - Nils-Ole Friedrich; Florian Flachsenberg; Agnes Meyder; Kai Sommer; Johannes Kirchmair; Matthias Rarey (J. Chem. Inf. Model., 2019)

Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms. - Robert Schmidt 002; Emanuel S. R. Ehmki; Farina Ohm; Hans-Christian Ehrlich; Andriy Mashychev; Matthias Rarey (J. Chem. Inf. Model., 2019)

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. - Jochen Sieg; Florian Flachsenberg; Matthias Rarey (J. Chem. Inf. Model., 2019)

A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. - Florian Flachsenberg; Agnes Meyder; Kai Sommer; Patrick Penner; Matthias Rarey (J. Chem. Inf. Model., 2020)

Editorial: Method and Data Sharing and Reproducibility of Scientific Results. - Kenneth M. Merz Jr.; Rommie E. Amaro; Zoe Cournia; Matthias Rarey; Thereza A. Soares; Alexander Tropsha; Habibah A. Wahab; Renxiao Wang (J. Chem. Inf. Model., 2020)

Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. - Patrick Penner; Virginie Y. Martiny; Arnaud Gohier; Marcus Gastreich; Pierre Ducrot; David Brown; Matthias Rarey (J. Chem. Inf. Model., 2020)

ProteinsPlus: interactive analysis of protein-ligand binding interfaces. - Katrin Schöning-Stierand; Konrad Diedrich; Rainer Fährrolfes; Florian Flachsenberg; Agnes Meyder; Eva Nittinger; Ruben Steinegger; Matthias Rarey (Nucleic Acids Res., 2020)

GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank. - Konrad Diedrich; Joel Graef; Katrin Schöning-Stierand; Matthias Rarey (Bioinform., 2021)

LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. - Florian Flachsenberg; Matthias Rarey (J. Comput. Chem., 2021)

Topological Similarity Search in Large Combinatorial Fragment Spaces. - Louis Bellmann; Patrick Penner; Matthias Rarey (J. Chem. Inf. Model., 2021)

Call for Papers for the Special Issue: From Reaction Informatics to Chemical Space. - Matthias Rarey; Marc C. Nicklaus; Wendy A. Warr (J. Chem. Inf. Model., 2021)

Disconnected Maximum Common Substructures under Constraints. - Robert Schmidt 002; Florian Krull; Anna Lina Heinzke; Matthias Rarey (J. Chem. Inf. Model., 2021)

FastGrow: on-the-fly growing and its application to DYRK1A. - Patrick Penner; Virginie Y. Martiny; Louis Bellmann; Florian Flachsenberg; Marcus Gastreich; Isabelle Theret; Christophe Meyer; Matthias Rarey (J. Comput. Aided Mol. Des., 2022)

Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces. - Louis Bellmann; Raphael Klein; Matthias Rarey (J. Chem. Inf. Model., 2022)

Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. - Louis Bellmann; Patrick Penner; Marcus Gastreich; Matthias Rarey (J. Chem. Inf. Model., 2022)

Synthesis-Aware Generation of Structural Analogues. - Uschi Dolfus; Hans Briem; Matthias Rarey (J. Chem. Inf. Model., 2022)

Visualizing Generic Reaction Patterns. - Uschi Dolfus; Hans Briem; Matthias Rarey (J. Chem. Inf. Model., 2022)

Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence. - Tobias Harren; Hans Matter; Gerhard Hessler; Matthias Rarey; Christoph Grebner (J. Chem. Inf. Model., 2022)

The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. - Patrick Penner; Wolfgang Guba; Robert Schmidt 002; Agnes Meyder; Martin Stahl; Matthias Rarey (J. Chem. Inf. Model., 2022)

Special Issue on Reaction Informatics and Chemical Space. - Matthias Rarey; Marc C. Nicklaus; Wendy A. Warr (J. Chem. Inf. Model., 2022)

Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces. - Robert Schmidt 002; Raphael Klein; Matthias Rarey (J. Chem. Inf. Model., 2022)

Exploration of Ultralarge Compound Collections for Drug Discovery. - Wendy A. Warr; Marc C. Nicklaus; Christos A. Nicolaou; Matthias Rarey (J. Chem. Inf. Model., 2022)

ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. - Katrin Schöning-Stierand; Konrad Diedrich; Christiane Ehrt; Florian Flachsenberg; Joel Graef; Jochen Sieg; Patrick Penner; Martin Poppinga; Annett Ungethüm; Matthias Rarey (Nucleic Acids Res., 2022)

Database and Workflow Optimizations for Spatial-Geometric Queries in GeoMine. - Martin Poppinga; Joel Graef; Konrad Diedrich; Matthias Rarey; Norbert Ritter (LWDA, 2023)

Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores. - Christian Meyenburg; Uschi Dolfus; Hans Briem; Matthias Rarey (J. Comput. Aided Mol. Des., 2023)

Modeling with Alternate Locations in X-ray Protein Structures. - Torben Gutermuth; Jochen Sieg; Tim Stohn; Matthias Rarey (J. Chem. Inf. Model., 2023)

Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3. - Joel Graef; Christiane Ehrt; Matthias Rarey (J. Chem. Inf. Model., 2023)

Optimization and Evaluation Datasets for PiMine. - Joel Graef; Christiane Ehrt; Thorben Reim; Matthias Rarey (UHH-FDR, 2023)

Single mutation protein structure pairs extracted from the PDB with MicroMiner. - Jochen Sieg; Matthias Rarey (UHH-FDR, 2023)

Searching similar local 3D micro-environments in protein structure databases with MicroMiner. - Jochen Sieg; Matthias Rarey (Briefings Bioinform., 2023)

PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams. - Konrad Diedrich; Bennet Krause; Ole Berg; Matthias Rarey (J. Comput. Aided Mol. Des., 2023)

Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures. - Uschi Dolfus; Hans Briem; Torben Gutermuth; Matthias Rarey (J. Chem. Inf. Model., 2023)

School of cheminformatics in Latin America. - 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 (J. Cheminformatics, 2023)

Database-Driven Identification of Structurally Similar Protein-Protein Interfaces. - Joel Graef; Christiane Ehrt; Thorben Reim; Matthias Rarey (J. Chem. Inf. Model., 2024)

Enhanced Calculation of Property Distributions in Chemical Fragment Spaces. - Justin Lübbers; Uta F. Lessel; Matthias Rarey (J. Chem. Inf. Model., 2024)

Optimization and Evaluation Datasets for PiMine. - Joel Graef; Christiane Ehrt; Thorben Reim; Matthias Rarey (UHH-FDR, 2024)

Optimization and Evaluation Datasets for PiMine. - Joel Graef; Christiane Ehrt; Thorben Reim; Matthias Rarey (UHH-FDR, 2024)

Redocking the PDB. - Florian Flachsenberg; Christiane Ehrt; Torben Gutermuth; Matthias Rarey (J. Chem. Inf. Model., 2024)

User-centric design of a 3D search interface for protein-ligand complexes. - Konrad Diedrich; Christiane Ehrt; Joel Graef; Martin Poppinga; Norbert Ritter; Matthias Rarey (J. Comput. Aided Mol. Des., 2024)

SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. - Sophia M. N. Hönig; Florian Flachsenberg; Christiane Ehrt; Alexander Neumann; Robert Schmidt 002; Christian Lemmen; Matthias Rarey (J. Comput. Aided Mol. Des., 2024)

Caching Partition Identifiers for Fast Geometric Pattern Matching. - Martin Poppinga; Annett Ungethüm; Matthias Rarey (BTW, 2025)

Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays. - Sophia M. N. Hönig; Torben Gutermuth; Christiane Ehrt; Christian Lemmen; Matthias Rarey (J. Comput. Aided Mol. Des., 2025)