M. Rarey

发表

A fast flexible docking method using an incremental construction algorithm.

Thomas Lengauer, G. Klebe, M. Rarey, 1996, Journal of molecular biology.

Computational methods for biomolecular docking.

Thomas Lengauer, M. Rarey, 1996, Current opinion in structural biology.

FlexE: efficient molecular docking considering protein structure variations.

Thomas Lengauer, M. Rarey, H. Claussen, 2001, Journal of molecular biology.

Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking

Thomas Lengauer, M. Rarey, B. Kramer, 1999, Proteins.

Review Special Focu S: computational chemi S t R y

M. Rarey, Andrea Volkamer, 2014 .

The particle concept: placing discrete water molecules during protein‐ligand docking predictions

T Lengauer, B Kramer, M Rarey, 1999, Proteins.

FlexX‐Scan: Fast, structure‐based virtual screening

M. Rarey, Ingo Schellhammer, 2004, Proteins.

SIENA: Efficient Compilation of Selective Protein Binding Site Ensembles

M. Rarey, Stefan Bietz, 2016, J. Chem. Inf. Model..

Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces.

M. Rarey, Stefan Bietz, G. Lange, 2017, Journal of medicinal chemistry.

Detailed analysis of scoring functions for virtual screening.

M Rarey, M Stahl, M. Rarey, 2001, Journal of medicinal chemistry.

Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function

Matthias Rarey, Ingo Reulecke, M. Rarey, 2008, ChemMedChem.

Torsion angle preferences in druglike chemical space: a comprehensive guide.

Matthias Rarey, Wolfgang Guba, Martin Stahl, 2013, Journal of medicinal chemistry.

Small Molecule Docking and Scoring

Matthias Rarey, Ingo Muegge, M. Rarey, 2001 .

Coping with Combinatorial Space in Molecular Design

M. Rarey, Florian Lauck, 2013 .

NAOMInext - Synthetically feasible fragment growing in a structure-based design context.

M. Rarey, Kai Sommer, Florian Flachsenberg, 2019, European journal of medicinal chemistry.

Matthias Rarey, Uta F. Lessel, J. Robert Fischer, 2010, J. Chem. Inf. Model..

In silico Design, Synthesis, and Screening of Novel Deoxyhypusine Synthase Inhibitors Targeting HIV‐1 Replication

J. Hauber, M. Rarey, C. Meier, 2014, ChemMedChem.

Modeling of metal interaction geometries for protein–ligand docking

Matthias Rarey, Andreas Kämper, Ingo Reulecke, 2007, Proteins.

From Activity Cliffs to Target‐Specific Scoring Models and Pharmacophore Hypotheses

Matthias Rarey, Markus Wagener, M. Rarey, 2011, ChemMedChem.

Perspectives from Medicinal Chemistry

G. Schneider, P. Willett, M. Rarey, 2012 .

Supporting Biocatalysis Research with Structural Bioinformatics

M. Rarey, Andrea Volkamer, E. Nittinger, 2016 .

Inhibition of SARS-CoV-2 main protease by allosteric drug-binding

Diana C. F. Monteiro, H. Chapman, C. Betzel, 2020, bioRxiv.

Massive X-ray screening reveals two allosteric drug binding sites of SARS-CoV-2 main protease

Diana C. F. Monteiro, H. Chapman, C. Betzel, 2020 .

Prediction of protein mutation effects based on dehydration and hydrogen bonding – A large‐scale study

M. Rarey, Stefan Bietz, G. Lange, 2017, Proteins.

ProteinsPlus: interactive analysis of protein–ligand binding interfaces

M. Rarey, E. Nittinger, Agnes Meyder, 2020, Nucleic Acids Res..

Computational Macrocyclization: From de novo Macrocycle Generation to Binding Affinity Estimation

Matthias Rarey, Kai Sommer, Hans Briem, 2017, ChemMedChem.

From Modeling to Medicinal Chemistry: Automatic Generation of Two‐Dimensional Complex Diagrams

Katrin Stierand, Matthias Rarey, M. Rarey, 2007, ChemMedChem.

Prediction, Analysis, and Comparison of Active Sites

Matthias Rarey, Stefan Bietz, Andrea Volkamer, 2018 .

Searching for Substructures in Fragment Spaces

Matthias Rarey, Andrea Volkamer, Hans-Christian Ehrlich, 2012, J. Chem. Inf. Model..

Computational biotechnology: prediction of competitive substrate inhibition of enzymes by buffer compounds with protein-ligand docking.

Matthias Rarey, An-Ping Zeng, Karen T Schomburg, 2012, Journal of biotechnology.

Cover Picture: From Activity Cliffs to Target‐Specific Scoring Models and Pharmacophore Hypotheses (ChemMedChem 9/2011)

Matthias Rarey, Markus Wagener, M. Rarey, 2011 .

Matthias Rarey, Louis Bellmann, Patrick Penner, 2020, J. Chem. Inf. Model..

Proceedings of the German Conference on Bioinformatics (GCB 2005), Hamburg, Germany, October 5-7, 2005

Matthias Rarey, Andrew E. Torda, Stefan Kurtz, 2005, German Conference on Bioinformatics.

SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering.

Matthias Rarey, M. Rarey, J. Fischer, 2007 .

Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces

Matthias Rarey, Angela M. Henzler, Hans-Christian Ehrlich, 2013, J. Chem. Inf. Model..

Flat and Easy: 2D Depiction of Protein‐Ligand Complexes

Katrin Stierand, Matthias Rarey, M. Rarey, 2011, Molecular informatics.

Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures

Matthias Rarey, Agnes Meyder, Eva Nittinger, 2017, J. Chem. Inf. Model..

Nearly no Scoring Function Without a Hansch‐Analysis

M. Rarey, G. Lange, Robert Klein, 2012, Molecular informatics.

Rational Drug Design—Screening and Synthesis of Potential Deoxyhypusine Synthase Inhibitors Targeting HIV-1 Replication

J. Hauber, M. Rarey, C. Meier, 2010 .

Screening of Drug Databases

Gerhard Klebe, Matthias Rarey, Martin Stahl, 2004 .

10th ICCS/GCC Conference: 40 Years of Cheminformatics

Matthias Rarey, Frank Oellien, Markus Wagener, 2015, J. Chem. Inf. Model..

Machine learning in drug discovery

Matthias Rarey, Sepp Hochreiter, Guenter Klambauer, 2018, Nature Biotechnology.

Letter from the Editors

Matthias Rarey, Alexander Tropsha, Kenneth M. Merz, 2015, J. Chem. Inf. Model..

Inside Cover: CONFECT: Conformations from an Expert Collection of Torsion Patterns (ChemMedChem 10/2013)

Matthias Rarey, Jérôme Hert, Therese Inhester, 2013 .

Computer Processing of Chemical Structure Information

Matthias Rarey, Thomas Engel, Oliver Sacher, 2018, Chemoinformatics.

Geometric Problems and Algorithms in Computer-Aided Molecular Design

Matthias Rarey, M. Rarey, 2002, GI Jahrestagung.

Protein–Ligand Docking in Drug Design

M. Rarey, 2004 .

Call for Papers for the Special Issue: From Reaction Informatics to Chemical Space

Matthias Rarey, Marc C. Nicklaus, Wendy Warr, 2021, J. Chem. Inf. Model..

Scientific Requirements for the Next-Generation Semantic Web-Based Chemogenomics and Systems Chemical Biology Molecular Information System OPS

Barbara Zdrazil, Antony J. Williams, Matthias Rarey, 2013 .

A consistent description of HYdrogen bond and DEhydration energies in protein–ligand complexes: methods behind the HYDE scoring function

Matthias Rarey, Robert Klein, Nadine Schneider, 2012, Journal of Computer-Aided Molecular Design.

Structure‐Based Virtual Screening

Matthias Rarey, Adrian Kolodzik, Nadine Schneider, 2018 .

Analyzing structural features of proteins from deep‐sea organisms

C. Lemmen, M. Rarey, A. Meents, 2022, Proteins.

Small molecule superposition: A comprehensive overview on pose scoring of the latest methods

C. Lemmen, M. Rarey, Sophia M. N. Hönig, 2022, WIREs Computational Molecular Science.

Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias

J. Hauber, M. Rarey, T. Brümmendorf, 2012, Investigational New Drugs.

FastGrow: on-the-fly growing and its application to DYRK1A

M. Rarey, V. Martiny, M. Gastreich, 2022, Journal of Computer-Aided Molecular Design.

Exploring Structure–Activity Relationships with Three‐Dimensional Matched Molecular Pairs—A Review

Emanuel S. R. Ehmki, M. Rarey, 2018, ChemMedChem.

Special Issue on Reaction Informatics and Chemical Space

M. Rarey, M. Nicklaus, W. Warr, 2022, J. Chem. Inf. Model..

Calculating and Optimizing Physicochemical Property Distributions of Large Combinatorial Fragment Spaces

M. Rarey, Louis Bellmann, Raphael Klein, 2022, J. Chem. Inf. Model..

Virtual Materiality: Collectors and Collection in the Brazilian Music Blogosphere

M. Rarey, L. Fullerton, 2012 .

Galileo: Three-dimensional searching in large combinatorial fragment spaces on the example of pharmacophores

M. Rarey, H. Briem, Christian Meyenburg, 2022, Journal of Computer-Aided Molecular Design.

Assemblage, Occlusion, and the Art of Survival in the Black Atlantic

M. Rarey, 2018, African Arts.

Shine: The Visual Economy of Light in African Diasporic Aesthetic Practice

M. Rarey, 2017, African Arts.

SwiFT: An Index Structure for Reduced Graph Descriptors in Virtual Screening and Clustering

Matthias Rarey, J. Robert Fischer, M. Rarey, 2007, J. Chem. Inf. Model..

ProteinsPlus: a web portal for structure analysis of macromolecules

Matthias Rarey, Agnes Meyder, Stefan Bietz, 2017, Nucleic Acids Res..

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment

Daniel Kuhn, Matthias Rarey, Friedrich Rippmann, 2012, Bioinform..

Molecular complexes at a glance: automated generation of two-dimensional complex diagrams

Katrin Stierand, Matthias Rarey, Patrick C. Maaß, 2006, Bioinform..

Combining Global and Local Measures for Structure-Based Druggability Predictions

Daniel Kuhn, Matthias Rarey, Friedrich Rippmann, 2012, J. Chem. Inf. Model..

Maximum Common Substructure Searching in Combinatorial Make-on-Demand Compound Spaces

M. Rarey, Robert Schmidt, Raphael Klein, 2021, J. Chem. Inf. Model..

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets

Matthias Rarey, Andrea Volkamer, Thomas Grombacher, 2010, J. Chem. Inf. Model..

Identification of Inhibitors of the Tyrosine Kinase c‐Met by Structure‐Based Virtual Screening

M. Rarey, F. Totzke, M. Kubbutat, 2011, Molecular informatics.

Maximum common subgraph isomorphism algorithms and their applications in molecular science: a review

Matthias Rarey, Hans-Christian Ehrlich, M. Rarey, 2011 .

NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures.

Matthias Rarey, Kai Sommer, Stefan Bietz, 2017, Journal of chemical information and modeling.

Torsion Library Reloaded: A New Version of Expert-Derived SMARTS Rules for Assessing Conformations of Small Molecules

Matthias Rarey, Wolfgang Guba, Agnes Meyder, 2016, J. Chem. Inf. Model..

Exploiting structural information for drug-target assessment.

Matthias Rarey, Andrea Volkamer, M. Rarey, 2014, Future medicinal chemistry.

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening

Matthias Rarey, Florian Flachsenberg, Jochen Sieg, 2019, J. Chem. Inf. Model..

On the Art of Compiling and Using 'Drug‐Like' Chemical Fragment Spaces

Matthias Rarey, Christof Wegscheid-Gerlach, Jörg Degen, 2008, ChemMedChem.

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

Holger Claussen, Matthias Rarey, Christian Lemmen, 2012, Journal of Computer-Aided Molecular Design.

Two-stage method for protein-ligand docking.

T Lengauer, B Kramer, M Rarey, 1999, Journal of medicinal chemistry.

Protein–ligand interaction databases: advanced tools to mine activity data and interactions on a structural level

Matthias Rarey, Therese Inhester, M. Rarey, 2014 .

A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community)

Arne Elofsson, Matthias Rarey, Anastassis Perrakis, 2020, F1000Research.

Scientific competency questions as the basis for semantically enriched open pharmacological space development.

Barbara Zdrazil, Matthias Rarey, Jordi Mestres, 2013, Drug discovery today.

A recursive algorithm for efficient combinatorial library docking

Thomas Lengauer, Matthias Rarey, Thomas Lengauer, 2000 .

Feature trees: A new molecular similarity measure based on tree matching

Matthias Rarey, J. Scott Dixon, J. S. Dixon, 1998, J. Comput. Aided Mol. Des..

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies

Thomas Lengauer, Matthias Rarey, Joannis Apostolakis, 2006, J. Chem. Inf. Model..

Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins

Thomas Lengauer, Matthias Rarey, Bernd Kramer, 1995, ISMB.

Linker‐Region Modified Derivatives of the Deoxyhypusine Synthase Inhibitor CNI‐1493 Suppress HIV‐1 Replication

J. Hauber, M. Rarey, J. van Lunzen, 2016, Archiv der Pharmazie.

Never at Rest: African Art at the University of Wisconsin

M. Rarey, H. Drewal, 2020, African Arts.

Predicting enzymatic function from global binding site descriptors

Daniel Kuhn, Matthias Rarey, Friedrich Rippmann, 2013, Proteins.

Black Mexico: Race and Society from Colonial to Modern Times

M. Rarey, Matthew Restall, B. Vinson, 2010 .

Feasibility of Active Machine Learning for Multiclass Compound Classification

Ulrike von Luxburg, Matthias Rarey, Florian Flachsenberg, 2016, J. Chem. Inf. Model..

Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease

Diana C. F. Monteiro, H. Chapman, C. Betzel, 2020, bioRxiv.

De novo design by pharmacophore-based searches in fragment spaces

Matthias Rarey, Wolfgang Guba, Tobias Lippert, 2011, J. Comput. Aided Mol. Des..

X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease

Diana C. F. Monteiro, H. Chapman, C. Betzel, 2021, Science.

Disconnected Maximum Common Substructures under Constraints

Matthias Rarey, Robert Schmidt, Florian Krull, 2020, J. Chem. Inf. Model..

MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing

Matthias Rarey, Matthias Hilbig, M. Rarey, 2015, J. Chem. Inf. Model..

MONA – Interactive manipulation of molecule collections

Matthias Rarey, Matthias Hilbig, Sascha Urbaczek, 2013, Journal of Cheminformatics.

Fast automated placement of polar hydrogen atoms in protein-ligand complexes

Matthias Rarey, Tobias Lippert, M. Rarey, 2009, J. Cheminformatics.

Facing the Challenges of Structure-Based Target Prediction by Inverse Virtual Screening

Matthias Rarey, Stefan Bietz, Karen Schomburg, 2014, J. Chem. Inf. Model..

Interpretation of Structure-Activity Relationships in Real-World Drug Design Data Sets Using Explainable Artificial Intelligence

C. Grebner, H. Matter, G. Hessler, 2022, J. Chem. Inf. Model..

Machine Learning in Drug Discovery

Matthias Rarey, Sepp Hochreiter, Günter Klambauer, 2018, Journal of Chemical Information and Modeling.

TFD: Torsion Fingerprints As a New Measure To Compare Small Molecule Conformations

Matthias Rarey, Wolfgang Guba, Tanja Schulz-Gasch, 2012, J. Chem. Inf. Model..

SMARTS.plus – A Toolbox for Chemical Pattern Design

Matthias Rarey, Emanuel S. R. Ehmki, Robert Schmidt, 2020, Molecular informatics.

Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes

Matthias Rarey, Stefan Bietz, Sascha Urbaczek, 2014, Journal of Cheminformatics.

Drawing the PDB: Protein-Ligand Complexes in Two Dimensions.

Katrin Stierand, Matthias Rarey, M. Rarey, 2010, ACS medicinal chemistry letters.

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources

Martin Vingron, Christian von Mering, Ines Liebich, 2004, Bioinform..

Protein Flexibility in Structure‐Based Virtual Screening: From Models to Algorithms

Matthias Rarey, Angela M. Henzler, M. Rarey, 2011 .

Flexible docking under pharmacophore type constraints

Thomas Lengauer, Matthias Rarey, Christian Buning, 2002, J. Comput. Aided Mol. Des..

Placement of medium-sized molecular fragments into active sites of proteins

Thomas Lengauer, Matthias Rarey, Stephan Wefing, 1996, J. Comput. Aided Mol. Des..

Protein pocket and ligand shape comparison and its application in virtual screening

Matthias Rarey, Friedrich Rippmann, Olivier Michielin, 2013, Journal of Computer-Aided Molecular Design.

Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis

Matthias Rarey, Emanuel S. R. Ehmki, Robert Schmidt, 2019, J. Chem. Inf. Model..

Systematic benchmark of substructure search in molecular graphs - From Ullmann to VF2

Matthias Rarey, Hans-Christian Ehrlich, M. Rarey, 2012, Journal of Cheminformatics.

NAOMI: On the Almost Trivial Task of Reading Molecules from Different File formats

Matthias Rarey, Sascha Urbaczek, Tobias Lippert, 2011, J. Chem. Inf. Model..

Automated Drawing of Structural Molecular Formulas under Constraints

Matthias Rarey, Marcus Gastreich, Patrick C. Fricker, 2004, J. Chem. Inf. Model..

Editorial: Method and Data Sharing and Reproducibility of Scientific Results

Rommie E. Amaro, A. Tropsha, M. Rarey, 2020, J. Chem. Inf. Model..

Matthias Rarey, Martin Stahl, M. Rarey, 2001, J. Comput. Aided Mol. Des..

Modeling with Alternate Locations in X-ray Protein Structures

M. Rarey, Jochen Sieg, Torben Gutermuth, 2023, J. Chem. Inf. Model..

From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library.

Matthias Rarey, Thomas Otto, Agnes Meyder, 2017, Journal of biotechnology.

PoseView -- molecular interaction patterns at a glance

Katrin Stierand, Matthias Rarey, M. Rarey, 2010, J. Cheminformatics.

Matthias Rarey, Uta F. Lessel, J. Robert Fischer, 2011, J. Chem. Inf. Model..

In Pursuit of Fully Flexible Protein‐Ligand Docking: Modeling the Bilateral Mechanism of Binding

Matthias Rarey, Angela M. Henzler, Angela M Henzler, 2010, Molecular informatics.

CASP2 experiences with docking flexible ligands using FLEXX

T Lengauer, B Kramer, M Rarey, 1997, Proteins.

Exploration of Ultralarge Compound Collections for Drug Discovery

M. Rarey, M. Nicklaus, W. Warr, 2022, J. Chem. Inf. Model..

Recore: A Fast and Versatile Method for Scaffold Hopping Based on Small Molecule Crystal Structure Conformations

Matthias Rarey, Martin Stahl, Tanja Schulz-Gasch, 2007, J. Chem. Inf. Model..

Novel technologies for virtual screening.

Thomas Lengauer, Matthias Rarey, Marc Zimmermann, 2004, Drug discovery today.

Unique Ring Families: A Chemically Meaningful Description of Molecular Ring Topologies

Matthias Rarey, Sascha Urbaczek, Adrian Kolodzik, 2012, J. Chem. Inf. Model..

From Structure Diagrams to Visual Chemical Patterns

Katrin Stierand, Matthias Rarey, Karen Schomburg, 2010, J. Chem. Inf. Model..

Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration

Matthias Rarey, Louis Bellmann, Patrick Penner, 2019, J. Chem. Inf. Model..

Design of Combinatorial Libraries for the Exploration of Virtual Hits from Fragment Space Searches with LoFT

Matthias Rarey, Uta F. Lessel, Bernd Wellenzohn, 2012, J. Chem. Inf. Model..

Exploring fragment spaces under multiple physicochemical constraints

Matthias Rarey, Juri Pärn, Jörg Degen, 2007, J. Comput. Aided Mol. Des..

FlexNovo: Structure‐Based Searching in Large Fragment Spaces

Matthias Rarey, Jörg Degen, M. Rarey, 2006, ChemMedChem.

Design and Diversity Analysis of Compound Libraries for Lead Discovery

Matthias Rarey, Hans Matter, H. Matter, 1999 .

mRAISE: an alternative algorithmic approach to ligand-based virtual screening

Matthias Rarey, Stefan Bietz, Eva Nittinger, 2016, Journal of Computer-Aided Molecular Design.

Benchmark Data Sets for Structure-Based Computational Target Prediction

Matthias Rarey, Karen Schomburg, M. Rarey, 2014, J. Chem. Inf. Model..

An integrated approach to knowledge-driven structure-based virtual screening

Matthias Rarey, Matthias Hilbig, Angela M. Henzler, 2014, Journal of Computer-Aided Molecular Design.

TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time

Matthias Rarey, Ingo Schellhammer, M. Rarey, 2007, J. Comput. Aided Mol. Des..

Navigating large chemical spaces in early-phase drug discovery.

M. Rarey, Fiorella Ruggiu, C. Ehrt, 2023, Current opinion in structural biology.

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations

Matthias Rarey, Stefan Bietz, M. Rarey, 2015, J. Chem. Inf. Model..

Consistent two-dimensional visualization of protein-ligand complex series

Katrin Stierand, Matthias Rarey, M. Rarey, 2011, J. Cheminformatics.

Interactive design of generic chemical patterns.

Matthias Rarey, Karen T Schomburg, Lars Wetzer, 2013, Drug discovery today.

11th German Conference on Chemoinformatics (GCC 2015)

Timothy Clark, Jonathan W. Essex, Peter Kolb, 2016, Journal of Cheminformatics.

Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density

Matthias Rarey, Eva Nittinger, Nadine Schneider, 2015, J. Chem. Inf. Model..

Conformator: A Novel Method for the Generation of Conformer Ensembles

Matthias Rarey, Agnes Meyder, Kai Sommer, 2019, J. Chem. Inf. Model..

Benchmarking Commercial Conformer Ensemble Generators

Matthias Rarey, Kai Sommer, Nils-Ole Friedrich, 2017, J. Chem. Inf. Model..

High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators

Matthias Rarey, Agnes Meyder, Kai Sommer, 2017, J. Chem. Inf. Model..

ProteinsPlus: a comprehensive collection of web-based molecular modeling tools

M. Rarey, C. Ehrt, Florian Flachsenberg, 2022, Nucleic Acids Res..

Second-generation de novo design: a view from a medicinal chemist perspective

Holger Claussen, Johann Gasteiger, Matthias Rarey, 2009, J. Comput. Aided Mol. Des..

FlexE: efficient molecular docking considering protein structure variations.

Thomas Lengauer, M. Rarey, H. Claussen, 2001, Journal of molecular biology.

Fast force field‐based optimization of protein–ligand complexes with graphics processor

Matthias Rarey, Robert Klein, Lennart Heinzerling, 2012, J. Comput. Chem..

Docking of hydrophobic ligands with interaction-based matching algorithms

Thomas Lengauer, Matthias Rarey, Bernd Kramer, 1999, German Conference on Bioinformatics.

Multiple automatic base selection: Protein–ligand docking based on incremental construction without manual intervention

Thomas Lengauer, Matthias Rarey, Bernd Kramer, 1997, J. Comput. Aided Mol. Des..

FSees: Customized Enumeration of Chemical Subspaces with Limited Main Memory Consumption

Matthias Rarey, Florian Lauck, M. Rarey, 2016, J. Chem. Inf. Model..

FlexE: efficient molecular docking considering protein structure variations.

Thomas Lengauer, M. Rarey, H. Claussen, 2001, Journal of molecular biology.

Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms

Matthias Rarey, Emanuel S. R. Ehmki, Robert Schmidt, 2019, J. Chem. Inf. Model..

What is the potential of structure-based target prediction methods?

Matthias Rarey, Karen T Schomburg, M. Rarey, 2014, Future medicinal chemistry.

Structure Based Drug Design

Thomas Lengauer, M. Rarey, B. Kramer, 2005 .

PoseEdit: enhanced ligand binding mode communication by interactive 2D diagrams

M. Rarey, K. Diedrich, Bennet Krause, 2023, Journal of Computer-Aided Molecular Design.

Binding Site Detection Remastered: Enabling Fast, Robust, and Reliable Binding Site Detection and Descriptor Calculation with DoGSite3

M. Rarey, C. Ehrt, Joel Graef, 2023, J. Chem. Inf. Model..

Searching Geometric Patterns in Protein Binding Sites and Their Application to Data Mining in Protein Kinase Structures.

M. Rarey, N. Ritter, C. Ehrt, 2021, Journal of medicinal chemistry.

GeoMine: interactive pattern mining of protein-ligand interfaces in the Protein Data Bank

Matthias Rarey, Konrad Diedrich, Joel Graef, 2020, Bioinform..

Scientific competency questions as the basis for semantically enriched open pharmacological space development.

Emiliano Cuadrado Rodríguez, Antony J. Williams, S. Pettifer, 2013, Drug discovery today.

Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web

Katrin Stierand, Matthias Rarey, Christian Lemmen, 2014, Journal of Cheminformatics.

Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples

Matthias Rarey, Stefan Bietz, Eva Nittinger, 2018, J. Chem. Inf. Model..

UNICON: A Powerful and Easy-to-Use Compound Library Converter

Matthias Rarey, Kai Sommer, Nils-Ole Friedrich, 2016, J. Chem. Inf. Model..

The Valence State Combination Model: A Generic Framework for Handling Tautomers and Protonation States

Matthias Rarey, Sascha Urbaczek, Adrian Kolodzik, 2014, J. Chem. Inf. Model..

Index-Based Searching of Interaction Patterns in Large Collections of Protein-Ligand Interfaces

Matthias Rarey, Robert Schmidt, Stefan Bietz, 2017, J. Chem. Inf. Model..

A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses

Matthias Rarey, Agnes Meyder, Kai Sommer, 2020, J. Chem. Inf. Model..

Exploiting structural information for drug-target assessment.

M. Rarey, Andrea Volkamer, 2014, Future medicinal chemistry.

Structure-Based Drug Design

Thomas Lengauer, M. Rarey, B. Kramer, 2013 .

Full Modification Control over Retrosynthetic Routes for Guided Optimization of Lead Structures

M. Rarey, Uschi Dolfus, Torben Gutermuth, 2023, J. Chem. Inf. Model..

School of cheminformatics in Latin America

M. Rarey, J. Medina‐Franco, Barbara Zdrazil, 2023, Journal of Cheminformatics.

Where are the boundaries? Automated pocket detection for druggability studies

Matthias Rarey, Andrea Volkamer, Thomas Grombacher, 2010, J. Cheminformatics.

Algorithmic Engines in Virtual Screening

Matthias Rarey, Christian Lemmen, Hans Matter, 2005 .

StructureProfiler: an all‐in‐one tool for 3D protein structure profiling

Matthias Rarey, Agnes Meyder, Nils-Ole Friedrich, 2018, Bioinform..