Works matching AU Rarey, Matthias

Results: 77

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

Published in:

Bioinformatics, 2012, v. 28, n. 15, p. 2074, doi. 10.1093/bioinformatics/bts310

By:

Volkamer, Andrea;
Kuhn, Daniel;
Rippmann, Friedrich;
Rarey, Matthias

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

Molecular Design. Concepts and Applications. By Gisbert Schneider and Karl-Heinz Baringhaus.

Published in:

Angewandte Chemie International Edition, 2009, v. 48, n. 10, p. 1718, doi. 10.1002/anie.200900047

By:

Rarey, Matthias

Publication type:

Article

LifeSoaks: a tool for analyzing solvent channels in protein crystals and obstacles for soaking experiments.

Published in:

Acta Crystallographica: Section D, Structural Biology, 2023, v. 79, n. 9, p. 837, doi. 10.1107/S205979832300582X

By:

Pletzer-Zelgert, Jonathan;
Ehrt, Christiane;
Fender, Inken;
Griewel, Axel;
Flachsenberg, Florian;
Klebe, Gerhard;
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

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

Published in:

Journal of Cheminformatics, 2012, v. 4, n. 1, p. 1, doi. 10.1186/1758-2946-4-13

By:

Ehrlich, Hans-Christian;
Rarey, Matthias

Publication type:

Article

Systematic search for pairwise dependencies of torsion angles.

Published in:

2012

By:

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

Publication type:

Abstract

A flexible-hydrogen interaction model for protein-ligand docking.

Published in:

2012

By:

Henzler, Angela M.;
Urbaczek, Sascha;
Schulz, Benjamin;
Rarey, Matthias

Publication type:

Abstract

Aligning chemical structure diagrams with local search.

Published in:

2012

By:

Hilbig, Matthias;
Rarey, Matthias

Publication type:

Abstract

Chemical pattern visualization in 2D-the SMARTSviewer.

Published in:

2011

By:

Schomburg, Karen;
Ehrlich, Hans-Christian;
Stierand, Katrin;
Rarey, Matthias

Publication type:

Abstract

PoseView - molecular interaction patterns at a glance.

Published in:

2010

By:

Stierand, Katrin;
Rarey, Matthias

Publication type:

Abstract

Where are the boundaries? Automated pocket detection for druggability studies.

Published in:

2010

By:

Volkamer, Andrea;
Grombacher, T.;
Rarey, Matthias

Publication type:

Abstract

Modeling of metal interaction geometries for protein-ligand docking.

Published in:

Proteins, 2008, v. 71, n. 3, p. 1237, doi. 10.1002/prot.21818

By:

Seebeck, Birte;
Reulecke, Ingo;
Kämper, Andreas;
Rarey, Matthias

Publication type:

Article

FlexX-Scan: Fast, structure-based virtual screening.

Published in:

Proteins, 2004, v. 57, n. 3, p. 504, doi. 10.1002/prot.20217

By:

Schellhammer, Ingo;
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

Searching similar local 3D micro-environments in protein structure databases with MicroMiner.

Published in:

Briefings in Bioinformatics, 2023, v. 24, n. 6, p. 1, doi. 10.1093/bib/bbad357

By:

Sieg, Jochen;
Rarey, Matthias

Publication type:

Article

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

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

Fast force field-based optimization of protein-ligand complexes with graphics processor.

Published in:

Journal of Computational Chemistry, 2012, v. 33, n. 32, p. 2554, doi. 10.1002/jcc.23094

By:

Heinzerling, Lennart;
Klein, Robert;
Rarey, Matthias

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

De novo design by pharmacophore-based searches in fragment spaces.

Published in:

Journal of Computer-Aided Molecular Design, 2011, v. 25, n. 10, p. 931, doi. 10.1007/s10822-011-9473-6

By:

Lippert, Tobias;
Schulz-Gasch, Tanja;
Roche, Olivier;
Guba, Wolfgang;
Rarey, Matthias

Publication type:

Article

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

Published in:

Journal of Computer-Aided Molecular Design, 2009, v. 23, n. 8, p. 593, doi. 10.1007/s10822-009-9291-2

By:

Zaliani, Andrea;
Boda, Krisztina;
Seidel, Thomas;
Herwig, Achim;
Schwab, Christof H.;
Gasteiger, Johann;
Claußen, Holger;
Lemmen, Christian;
Degen, Jörg;
Pärn, Juri;
Rarey, Matthias

Publication type:

Article

Exploring fragment spaces under multiple physicochemical constraints.

Published in:

Journal of Computer-Aided Molecular Design, 2007, v. 21, n. 6, p. 327, doi. 10.1007/s10822-007-9121-3

By:

Pärn, Juri;
Degen, Jörg;
Rarey, Matthias

Publication type:

Article