Works by Rarey, Matthias

Results: 77

SiteMine: Large‐scale binding site similarity searching in protein structure databases.

Published in:

Archiv der Pharmazie, 2024, v. 357, n. 5, p. 1, doi. 10.1002/ardp.202300661

By:

Reim, Thorben;
Ehrt, Christiane;
Graef, Joel;
Günther, Sebastian;
Meents, Alke;
Rarey, Matthias

Publication type:

Article

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

Published in:

Archiv der Pharmazie, 2016, v. 349, n. 2, p. 91, doi. 10.1002/ardp.201500323

By:

Schröder, Marcus;
Kolodzik, Adrian;
Windshügel, Björn;
Krepstakies, Marcel;
Priyadarshini, Poornima;
Hartjen, Philip;
van Lunzen, Jan;
Rarey, Matthias;
Hauber, Joachim;
Meier, Chris

Publication type:

Article

Evaluation of deoxyhypusine synthase inhibitors targeting BCR-ABL positive leukemias.

Published in:

Investigational New Drugs, 2012, v. 30, n. 6, p. 2274, doi. 10.1007/s10637-012-9810-1

By:

Ziegler, Patrick;
Chahoud, Tuhama;
Wilhelm, Thomas;
Pällman, Nora;
Braig, Melanie;
Wiehle, Valeska;
Ziegler, Susanne;
Schröder, Marcus;
Meier, Chris;
Kolodzik, Adrian;
Rarey, Matthias;
Panse, Jens;
Hauber, Joachim;
Balabanov, Stefan;
Brümmendorf, Tim

Publication type:

Article

SMARTS.plus – A Toolbox for Chemical Pattern Design.

Published in:

Molecular Informatics, 2020, v. 39, n. 12, p. 1, doi. 10.1002/minf.202000216

By:

Ehrt, Christiane;
Krause, Bennet;
Schmidt, Robert;
Ehmki, Emanuel S. R.;
Rarey, Matthias

Publication type:

Article

Corrigendum: The Art of Compiling Protein Binding Site Ensembles.

Published in:

Molecular Informatics, 2017, v. 36, n. 1/2, p. n/a, doi. 10.1002/minf.201780141

By:

Bietz, Stefan;
Fährrolfes, Rainer;
Rarey, Matthias

Publication type:

Article

The Art of Compiling Protein Binding Site Ensembles.

Published in:

Molecular Informatics, 2016, v. 35, n. 11/12, p. 593, doi. 10.1002/minf.201600043

By:

Bietz, Stefan;
Fährrolfes, Rainer;
Rarey, Matthias

Publication type:

Article

The Internet as Scientific Knowledge Base: Navigating the Chem-Bio Space.

Published in:

Molecular Informatics, 2012, v. 31, n. 8, p. 543, doi. 10.1002/minf.201200037

By:

Stierand, Katrin;
Harder, Tim;
Marek, Thomas;
Hilbig, Matthias;
Lemmen, Christian;
Rarey, Matthias

Publication type:

Article

Nearly no Scoring Function Without a Hansch-Analysis.

Published in:

Molecular Informatics, 2012, v. 31, n. 6/7, p. 503, doi. 10.1002/minf.201200022

By:

Schneider, Nadine;
Klein, Robert;
Lange, Gudrun;
Rarey, Matthias

Publication type:

Article

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

Published in:

Molecular Informatics, 2011, v. 30, n. 2/3, p. 145, doi. 10.1002/minf.201000138

By:

Lemcke, Thomas;
Dreher, Jan;
Rarey, Matthias;
Totzke, Frank;
Schächtele, Christoph;
Kubbutat, Michael H. G.;
Kunick, Conrad

Publication type:

Article

Flat and Easy: 2D Depiction of Protein-Ligand Complexes.

Published in:

Molecular Informatics, 2011, v. 30, n. 1, p. 12, doi. 10.1002/minf.201000167

By:

Stierand, Katrin;
Rarey, Matthias

Publication type:

Article

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

Published in:

Molecular Informatics, 2010, v. 29, n. 3, p. 164, doi. 10.1002/minf.200900078

By:

Henzler, Angela M.;
Rarey, Matthias

Publication type:

Article

Evaluation of the F LEXX incremental construction algorithm for protein-ligand docking.

Published in:

Proteins, 1999, v. 37, n. 2, p. 228, doi. 10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8

By:

Kramer, Bernd;
Rarey, Matthias;
Lengauer, Thomas

Publication type:

Article

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

Published in:

Proteins, 1999, v. 34, n. 1, p. 17, doi. 10.1002/(SICI)1097-0134(19990101)34:1<17::AID-PROT3>3.0.CO;2-1

By:

Rarey, Matthias;
Kramer, Bernd;
Lengauer, Thomas

Publication type:

Article

CASP2 experiences with docking flexible ligands using F LEXX.

Published in:

Proteins, 1997, v. 29, n. S1, p. 221, doi. 10.1002/(SICI)1097-0134(1997)1+<221::AID-PROT30>3.0.CO;2-O

By:

Kramer, Bernd;
Rarey, Matthias;
Lengauer, Thomas

Publication type:

Article

Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays.

Published in:

Journal of Computer-Aided Molecular Design, 2025, v. 39, n. 1, p. 1, doi. 10.1007/s10822-024-00581-1

By:

Hönig, Sophia M. N.;
Gutermuth, Torben;
Ehrt, Christiane;
Lemmen, Christian;
Rarey, Matthias

Publication type:

Article

User-centric design of a 3D search interface for protein-ligand complexes.

Published in:

Journal of Computer-Aided Molecular Design, 2024, v. 38, n. 1, p. 1, doi. 10.1007/s10822-024-00563-3

By:

Diedrich, Konrad;
Ehrt, Christiane;
Graef, Joel;
Poppinga, Martin;
Ritter, Norbert;
Rarey, Matthias

Publication type:

Article

SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces.

Published in:

Journal of Computer-Aided Molecular Design, 2024, v. 38, n. 1, p. 1, doi. 10.1007/s10822-024-00551-7

By:

Hönig, Sophia M. N.;
Flachsenberg, Florian;
Ehrt, Christiane;
Neumann, Alexander;
Schmidt, Robert;
Lemmen, Christian;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2023, v. 37, n. 10, p. 491, doi. 10.1007/s10822-023-00522-4

By:

Diedrich, Konrad;
Krause, Bennet;
Berg, Ole;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2023, v. 37, n. 1, p. 1, doi. 10.1007/s10822-022-00485-y

By:

Meyenburg, Christian;
Dolfus, Uschi;
Briem, Hans;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2022, v. 36, n. 9, p. 639, doi. 10.1007/s10822-022-00469-y

By:

Penner, Patrick;
Martiny, Virginie;
Bellmann, Louis;
Flachsenberg, Florian;
Gastreich, Marcus;
Theret, Isabelle;
Meyer, Christophe;
Rarey, Matthias

Publication type:

Article

Ligand-based virtual screening under partial shape constraints.

Published in:

Journal of Computer-Aided Molecular Design, 2017, v. 31, n. 4, p. 335, doi. 10.1007/s10822-017-0011-z

By:

Behren, Mathias;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2016, v. 30, n. 8, p. 583, doi. 10.1007/s10822-016-9940-1

By:

Behren, Mathias;
Bietz, Stefan;
Nittinger, Eva;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2014, v. 28, n. 9, p. 927, doi. 10.1007/s10822-014-9769-4

By:

Henzler, Angela;
Urbaczek, Sascha;
Hilbig, Matthias;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2013, v. 27, n. 6, p. 511, doi. 10.1007/s10822-013-9659-1

By:

Wirth, Matthias;
Volkamer, Andrea;
Zoete, Vincent;
Rippmann, Friedrich;
Michielin, Olivier;
Rarey, Matthias;
Sauer, Wolfgang

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2013, v. 27, n. 1, p. 15, doi. 10.1007/s10822-012-9626-2

By:

Schneider, Nadine;
Lange, Gudrun;
Hindle, Sally;
Klein, Robert;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2012, v. 26, n. 6, p. 701, doi. 10.1007/s10822-011-9531-0

By:

Schneider, Nadine;
Hindle, Sally;
Lange, Gudrun;
Klein, Robert;
Albrecht, Jürgen;
Briem, Hans;
Beyer, Kristin;
Claußen, Holger;
Gastreich, Marcus;
Lemmen, Christian;
Rarey, Matthias

Publication type:

Article

Some thoughts on the 'A' in computer-aided molecular design.

Published in:

Journal of Computer-Aided Molecular Design, 2012, v. 26, n. 1, p. 113, doi. 10.1007/s10822-011-9507-0

By:

Rarey, Matthias

Publication type:

Article

School of cheminformatics in Latin America.

Published in:

Journal of Cheminformatics, 2023, v. 15, n. 1, p. 1, doi. 10.1186/s13321-023-00758-0

By:

Gonzalez-Ponce, Karla;
Horta Andrade, Carolina;
Hunter, Fiona;
Kirchmair, Johannes;
Martinez-Mayorga, Karina;
Medina-Franco, José L.;
Rarey, Matthias;
Tropsha, Alexander;
Varnek, Alexandre;
Zdrazil, Barbara

Publication type:

Article

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

Published in:

ChemMedChem, 2018, v. 13, n. 6, p. 482, doi. 10.1002/cmdc.201700628

By:

Ehmki, Emanuel S. R.;
Rarey, Matthias

Publication type:

Article

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

Published in:

ChemMedChem, 2017, v. 12, n. 22, p. 1866, doi. 10.1002/cmdc.201700478

By:

Wagner, Vincent;
Jantz, Linda;
Briem, Hans;
Sommer, Kai;
Rarey, Matthias;
Christ, Clara D.

Publication type:

Article

Modern machine‐learning for binding affinity estimation of protein–ligand complexes: Progress, opportunities, and challenges.

Published in:

WIREs: Computational Molecular Science, 2024, v. 14, n. 3, p. 1, doi. 10.1002/wcms.1716

By:

Harren, Tobias;
Gutermuth, Torben;
Grebner, Christoph;
Hessler, Gerhard;
Rarey, Matthias

Publication type:

Article

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

Published in:

WIREs: Computational Molecular Science, 2023, v. 13, n. 2, p. 1, doi. 10.1002/wcms.1640

By:

Hönig, Sophia M. N.;
Lemmen, Christian;
Rarey, Matthias

Publication type:

Article

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

Published in:

WIREs: Computational Molecular Science, 2014, v. 4, n. 6, p. 562, doi. 10.1002/wcms.1192

By:

Inhester, Therese;
Rarey, Matthias

Publication type:

Article

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

Published in:

WIREs: Computational Molecular Science, 2011, v. 1, n. 1, p. 68, doi. 10.1002/wcms.5

By:

Ehrlich, Hans-Christian;
Rarey, Matthias

Publication type:

Article

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

Published in:

ChemMedChem, 2014, v. 9, n. 5, p. 940, doi. 10.1002/cmdc.201300481

By:

Schroeder, Marcus;
Kolodzik, Adrian;
Pfaff, Katharina;
Priyadarshini, Poornima;
Krepstakies, Marcel;
Hauber, Joachim;
Rarey, Matthias;
Meier, Chris

Publication type:

Article

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

Published in:

ChemMedChem, 2013, v. 8, n. 10, p. 1574, doi. 10.1002/cmdc.201390041

By:

Schärfer, Christin;
Schulz‐Gasch, Tanja;
Hert, Jérôme;
Heinzerling, Lennart;
Schulz, Benjamin;
Inhester, Therese;
Stahl, Martin;
Rarey, Matthias

Publication type:

Article

CONFECT: Conformations from an Expert Collection of Torsion Patterns.

Published in:

ChemMedChem, 2013, v. 8, n. 10, p. 1690, doi. 10.1002/cmdc.201300242

By:

Schärfer, Christin;
Schulz‐Gasch, Tanja;
Hert, Jérôme;
Heinzerling, Lennart;
Schulz, Benjamin;
Inhester, Therese;
Stahl, Martin;
Rarey, Matthias

Publication type:

Article

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

Published in:

ChemMedChem, 2011, v. 6, n. 9, p. 1533, doi. 10.1002/cmdc.201190037

By:

Seebeck, Birte;
Wagener, Markus;
Rarey, Matthias

Publication type:

Article

From Activity Cliffs to Target-Specific Scoring Models and Pharmacophore Hypotheses.

Published in:

ChemMedChem, 2011, v. 6, n. 9, p. 1630, doi. 10.1002/cmdc.201100179

By:

Seebeck, Birte;
Wagener, Markus;
Rarey, Matthias

Publication type:

Article

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

Published in:

ChemMedChem, 2008, v. 3, n. 10, p. 1503, doi. 10.1002/cmdc.200800178

By:

Degen, Jörg;
Wegscheid-Gerlach, Christof;
Zaliani, Andrea;
Rarey, Matthias

Publication type:

Article

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

Published in:

ChemMedChem, 2008, v. 3, n. 6, p. 885, doi. 10.1002/cmdc.200700319

By:

Reulecke, Ingo;
Lange, Gudrun;
Albrecht, Jürgen;
Klein, Robert;
Rarey, Matthias

Publication type:

Article

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

Published in:

ChemMedChem, 2007, v. 2, n. 6, p. 853, doi. 10.1002/cmdc.200700010

By:

Stierand, Katrin;
Rarey, Matthias

Publication type:

Article

FlexNovo: Structure-Based Searching in Large Fragment Spaces.

Published in:

ChemMedChem, 2006, v. 1, n. 8, p. 854, doi. 10.1002/cmdc.200500102

By:

Degen, Jörg;
Rarey, Matthias

Publication type:

Article

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

Published in:

2014

By:

Stierand, Katrin;
Harder, Tim;
Wissler, Lothar;
Lemmen, Christian;
Rarey, Matthias

Publication type:

Abstract

Elucidating protein-protein interactions using the HYDE scoring function.

Published in:

2014

By:

Vennmann, Eva;
Schneider, Nadine;
Lange, Gudrun;
Rarey, Matthias

Publication type:

Abstract

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

Published in:

Journal of Cheminformatics, 2014, v. 6, n. 1, p. 1, doi. 10.1186/1758-2946-6-12

By:

Bietz, Stefan;
Urbaczek, Sascha;
Schulz, Benjamin;
Rarey, Matthias

Publication type:

Article

MONA -- Interactive manipulation of molecule collections.

Published in:

Journal of Cheminformatics, 2013, v. 5, n. 1, p. 1, doi. 10.1186/1758-2946-5-38

By:

Hilbig, Matthias;
Urbaczek, Sascha;
Groth, Inken;
Heuser, Stefan;
Rarey, Matthias

Publication type:

Article

Force-field-based minimizations of protein-ligand complexes in the blink of an eye.

Published in:

2013

By:

Heinzerling, Lennart;
Rarey, Matthias

Publication type:

Conference Paper/Materials

TorsionAnalyzer: exploring conformational space.

Published in:

Journal of Cheminformatics, 2013, v. 5, n. S1, p. 1, doi. 10.1186/1758-2946-5-S1-P3

By:

Schärfer, Christin;
Schulz-Gasch, Tanja;
Rarey, Matthias

Publication type:

Article

Let's talk about rings.

Published in:

Journal of Cheminformatics, 2013, v. 5, n. S1, p. 1, doi. 10.1186/1758-2946-5-S1-O8

By:

Rarey, Matthias;
Kolodzik, Adrian;
Urbaczek, Sascha

Publication type:

Article