Matthias Rarey: search on Z-Library

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1

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

Friedrich, Nils-Ole, Meyder, Agnes, de Bruyn Kops, Christina, Sommer, Kai, Flachsenberg, Florian, Rarey, Matthias, Kirchmair, Johannes

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 1.60 MB

english, 2017

2

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

Urbaczek, Sascha, Kolodzik, Adrian, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 1.35 MB

english, 2014

3

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

Sieg, Jochen, Flachsenberg, Florian, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 2.57 MB

2019

4

Novel technologies for virtual screening

Thomas Lengauer, Christian Lemmen, Matthias Rarey, Marc Zimmermann

Journal:

Drug Discovery Today

Year:

2004

Language:

english

File:

PDF, 220 KB

english, 2004

5

Modeling of metal interaction geometries for protein–ligand docking

Birte Seebeck, Ingo Reulecke, Andreas Kämper, Matthias Rarey

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2008

Language:

english

File:

PDF, 588 KB

english, 2008

6

Ligand-based virtual screening under partial shape constraints

von Behren, Mathias M., Rarey, Matthias

Journal:

Journal of Computer-Aided Molecular Design

Year:

2017

Language:

english

File:

PDF, 1.73 MB

english, 2017

7

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

Inhester, Therese, Rarey, Matthias

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2014

Language:

english

File:

PDF, 334 KB

english, 2014

8

Some thoughts on the “A” in computer-aided molecular design

Journal:

Journal of Computer-Aided Molecular Design

Year:

2012

Language:

english

File:

PDF, 102 KB

english, 2012

9

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

Hans-Christian Ehrlich, Matthias Rarey

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2011

Language:

english

File:

PDF, 208 KB

english, 2011

10

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

Schomburg, Karen T., Bietz, Stefan, Briem, Hans, Henzler, Angela M., Urbaczek, Sascha, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 4.73 MB

english, 2014

11

CASP2 experiences with docking flexible ligands using FLEXX

Kramer, Bernd, Rarey, Matthias, Lengauer, Thomas

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 59 KB

english, 1997

12

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

Hans-Christian Ehrlich, Matthias Rarey

Journal:

Journal of Cheminformatics

Year:

2012

Language:

english

File:

PDF, 602 KB

english, 2012

13

ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations

Bietz, Stefan, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 2.36 MB

english, 2015

14

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, Christian Lemmen, Jörg Degen, Juri Pärn, Matthias Rarey

Journal:

Journal of Computer-Aided Molecular Design

Year:

2009

Language:

english

File:

PDF, 478 KB

english, 2009

15

Benchmark Data Sets for Structure-Based Computational Target Prediction

Schomburg, Karen T., Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 7.64 MB

english, 2014

16

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

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

Journal:

Archiv der Pharmazie

Year:

2016

Language:

english

File:

PDF, 1.45 MB

english, 2016

17

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

Nittinger, Eva, Flachsenberg, Florian, Bietz, Stefan, Lange, Gudrun, Klein, Robert, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 5.84 MB

english, 2018

18

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

Birte Seebeck, Dr. Markus Wagener, Prof. Dr. Matthias Rarey

Journal:

Year:

2011

Language:

english

File:

PDF, 2.32 MB

english, 2011

19

Nearly no Scoring Function Without a Hansch-Analysis

Nadine Schneider, Robert Klein, Gudrun Lange, Matthias Rarey

Journal:

Molecular Informatics

Year:

2012

Language:

english

File:

PDF, 666 KB

english, 2012

20

Shape-Based Descriptors for Efficient Structure-Based Fragment Growing

Penner, Patrick, Martiny, Virginie, Gohier, Arnaud, Gastreich, Marcus, Ducrot, Pierre, Brown, David, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 8.19 MB

2020

21

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

Matthias Rarey, J. Scott Dixon

Journal:

Journal of Computer-Aided Molecular Design

Year:

1998

Language:

english

File:

PDF, 233 KB

english, 1998

22

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

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

Journal:

Journal of Computer-Aided Molecular Design

Year:

2012

Language:

english

File:

PDF, 1.52 MB

english, 2012

23

Searching for Substructures in Fragment Spaces

Ehrlich, Hans-Christian, Volkamer, Andrea, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 1.14 MB

english, 2012

24

Detailed Analysis of Scoring Functions for Virtual Screening

Stahl, Martin, Rarey, Matthias

Journal:

Journal of Medicinal Chemistry

Year:

2001

Language:

english

File:

PDF, 220 KB

english, 2001

25

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

Maass, Patrick, Schulz-Gasch, Tanja, Stahl, Martin, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 349 KB

english, 2007

26

Conformator: A Novel Method for the Generation of Conformer Ensembles

Friedrich, Nils-Ole, Flachsenberg, Florian, Meyder, Agnes, Sommer, Kai, Kirchmair, Johannes, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 2.00 MB

english, 2019

27

Automated Drawing of Structural Molecular Formulas under Constraints.

Patrick C. Fricker, Marcus Gastreich, Matthias Rarey

Journal:

Year:

2004

File:

PDF, 60 KB

2004

28

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

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

Journal:

Year:

2008

Language:

english

File:

PDF, 334 KB

english, 2008

29

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

Angela M. Henzler, Matthias Rarey

Journal:

Molecular Informatics

Year:

2010

Language:

english

File:

PDF, 531 KB

english, 2010

30

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

Bernd Kramer, Matthias Rarey, Thomas Lengauer

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 822 KB

english, 1999

31

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

Katrin Stierand, Matthias Rarey

Journal:

Molecular Informatics

Year:

2011

Language:

english

File:

PDF, 670 KB

english, 2011

32

Two-Stage Method for Protein−Ligand Docking

Hoffmann, Daniel, Kramer, Bernd, Washio, Takumi, Steinmetzer, Torsten, Rarey, Matthias, Lengauer, Thomas

Journal:

Journal of Medicinal Chemistry

Year:

1999

Language:

english

File:

PDF, 217 KB

english, 1999

33

SMARTS.plus â A Toolbox for Chemical Pattern Design

Ehrt, Christiane, Krause, Bennet, Schmidt, Robert, Ehmki, Emanuel, Rarey, Matthias

Journal:

Molecular Informatics

Year:

2020

File:

PDF, 834 KB

2020

34

FlexNovo: Structure-Based Searching in Large Fragment Spaces

Jörg Degen, Matthias Rarey

Journal:

Year:

2006

Language:

english

File:

PDF, 1.02 MB

english, 2006

35

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

Birte Seebeck, Dr. Markus Wagener, Prof. Dr. Matthias Rarey

Journal:

Year:

2011

File:

PDF, 856 KB

2011

36

De novo design by pharmacophore-based searches in fragment spaces

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

Journal:

Journal of Computer-Aided Molecular Design

Year:

2011

Language:

english

File:

PDF, 1.16 MB

english, 2011

37

Exploring fragment spaces under multiple physicochemical constraints

Juri Pärn, Jörg Degen, Matthias Rarey

Journal:

Journal of Computer-Aided Molecular Design

Year:

2007

Language:

english

File:

PDF, 641 KB

english, 2007

38

Predicting enzymatic function from global binding site descriptors

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

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 23.76 MB

english, 2013

39

Let's talk about rings

Matthias Rarey, Adrian Kolodzik, Sascha Urbaczek

Journal:

Journal of Cheminformatics

Year:

2013

Language:

english

File:

PDF, 73 KB

english, 2013

40

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

Lennart Heinzerling, Matthias Rarey

Journal:

Journal of Cheminformatics

Year:

2013

Language:

english

File:

PDF, 69 KB

english, 2013

41

Elucidating protein-protein interactions using the HYDE scoring function

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

Journal:

Journal of Cheminformatics

Year:

2014

Language:

english

File:

PDF, 73 KB

english, 2014

42

Searching for Recursively Defined Generic Chemical Patterns in Nonenumerated Fragment Spaces

Ehrlich, Hans-Christian, Henzler, Angela M., Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 2.34 MB

english, 2013

43

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

Nittinger, Eva, Schneider, Nadine, Lange, Gudrun, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 5.88 MB

english, 2015

44

Topological Similarity Search in Large Combinatorial Fragment Spaces

Bellmann, Louis, Penner, Patrick, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 1.67 MB

2020

45

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

Marcus Schroeder, Adrian Kolodzik, Bjoern Windshuegel, Marcel Krepstakies, Poornima Priyadarshini, Matthias Rarey, Joachim Hauber, Chris Meier

Journal:

Antiviral Research

Year:

2010

Language:

english

File:

PDF, 74 KB

english, 2010

46

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

Kolodzik, Adrian, Urbaczek, Sascha, Rarey, Matthias

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 1.98 MB

english, 2012

47

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

Guba, Wolfgang, Meyder, Agnes, Rarey, Matthias, Hert, Jérôme

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 1.28 MB

english, 2015

48

Where are the boundaries? Automated pocket detection for druggability studies

Andrea Volkamer, T Grombacher, Matthias Rarey

Journal:

Journal of Cheminformatics

Year:

2010

Language:

english

File:

PDF, 147 KB

english, 2010

49

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

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

Journal:

Year:

2014

Language:

english

File:

PDF, 1.21 MB

english, 2014

50

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

Henzler, Angela M., Urbaczek, Sascha, Hilbig, Matthias, Rarey, Matthias

Journal:

Journal of Computer-Aided Molecular Design

Year:

2014

Language:

english

File:

PDF, 1.01 MB

english, 2014

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