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1

Computational Exploration of Molecular Scaffolds in Medicinal Chemistry

Hu, Ye, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2016

Language:

english

File:

PDF, 2.24 MB

english, 2016

2

Molecular Similarity in Medicinal Chemistry

Maggiora, Gerald, Vogt, Martin, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 2.68 MB

english, 2014

3

Computational Method for the Systematic Identification of Analog Series and Key Compounds Representing Series and Their Biological Activity Profiles

Stumpfe, Dagmar, Dimova, Dilyana, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2016

Language:

english

File:

PDF, 1.62 MB

english, 2016

4

Charting Biologically Relevant Spirocyclic Compound Space

Müller, Gerhard, Berkenbosch, Tim, Benningshof, Jorg, Stumpfe, Dagmar, Bajorath, Juergen

Journal:

Chemistry - A European Journal

Year:

2016

Language:

english

File:

PDF, 5.25 MB

english, 2016

5

Recent Advances in Scaffold Hopping

Hu, Ye, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2017

Language:

english

File:

PDF, 1.61 MB

english, 2017

6

Series of screening compounds with high hit rates for the exploration of multi-target activities and assay interference

Stumpfe, Dagmar, Gilberg, Erik, Bajorath, Jürgen

Journal:

Future Science OA

Year:

2018

Language:

english

File:

PDF, 318 KB

english, 2018

7

Redundancy in two major compound databases

Yonchev, Dimitar, Dimova, Dilyana, Stumpfe, Dagmar, Vogt, Martin, Bajorath, Jürgen

Journal:

Drug Discovery Today

Year:

2018

Language:

english

File:

PDF, 467 KB

english, 2018

8

Computational method for the identification of third generation activity cliffs

Stumpfe, Dagmar, Hu, Huabin, Bajorath, Jürgen

Journal:

Year:

2020

Language:

english

File:

PDF, 776 KB

english, 2020

9

Systematic Data Analysis and Diagnostic Machine Learning Reveal Differences between Compounds with Single- and Multitarget Activity

Feldmann, Christian, Yonchev, Dimitar, Stumpfe, Dagmar, Bajorath, JÃ¼rgen

Journal:

Molecular Pharmaceutics

Year:

2020

File:

PDF, 3.02 MB

2020

10

Hit Expansion through Computational Selectivity Searching

Dagmar Stumpfe, Maxim Frizler, Mihiret T. Sisay, José Batista, Ingo Vogt, Michael Gütschow, Jürgen Bajorath

Journal:

Year:

2009

Language:

english

File:

PDF, 175 KB

english, 2009

11

Inhibitors of Cathepsins K and S Identified Using the DynaMAD Virtual Screening Algorithm

Dagmar Stumpfe, Mihiret T. Sisay, Maxim Frizler, Ingo Vogt, Michael Gütschow, Jürgen Bajorath

Journal:

Year:

2010

Language:

english

File:

PDF, 329 KB

english, 2010

12

Methods for Computer-aided Chemical Biology. Part 2: Evaluation of Compound Selectivity Using 2D Molecular Fingerprints

Ingo Vogt, Dagmar Stumpfe, Hany E. A. Ahmed, Jürgen Bajorath

Journal:

Chemical Biology & Drug Design

Year:

2007

Language:

english

File:

PDF, 1.36 MB

english, 2007

13

Methods for Computer-aided Chemical Biology. Part 1: Design of a Benchmark System for the Evaluation of Compound Selectivity

Dagmar Stumpfe, Hany E. A. Ahmed, Ingo Vogt, Jürgen Bajorath

Journal:

Chemical Biology & Drug Design

Year:

2007

Language:

english

File:

PDF, 1.92 MB

english, 2007

14

Methods for Computer-Aided Chemical Biology. Part 3: Analysis of Structure–Selectivity Relationships through Single- or Dual-Step Selectivity Searching and Bayesian Classification

Dagmar Stumpfe, Hanna Geppert, Jürgen Bajorath

Journal:

Chemical Biology & Drug Design

Year:

2008

Language:

english

File:

PDF, 695 KB

english, 2008

15

Methods for Computer-Aided Chemical Biology. Part 4: Selectivity Searching for Ion Channel Ligands and Mapping of Molecular Fragments as Selectivity Markers

Hany E. A. Ahmed, Hanna Geppert, Dagmar Stumpfe, Eugen Lounkine, Jürgen Bajorath

Journal:

Chemical Biology & Drug Design

Year:

2009

Language:

english

File:

PDF, 907 KB

english, 2009

16

Lessons Learned from Molecular Scaffold Analysis

Hu, Ye, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2011

Language:

english

File:

PDF, 1.19 MB

english, 2011

17

Analysis of structure-based virtual screening studies and characterization of identified active compounds

Ripphausen, Peter, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Future Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

18

ChemInform Abstract: Methods for SAR Visualization

Dagmar Stumpfe, Juergen Bajorath

Journal:

Year:

2012

File:

PDF, 18 KB

2012

19

Similarity searching

Dagmar Stumpfe, Jürgen Bajorath

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2011

Language:

english

File:

PDF, 903 KB

english, 2011

20

Frequency of Occurrence and Potency Range Distribution of Activity Cliffs in Bioactive Compounds

Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 1.66 MB

english, 2012

21

Exploring Activity Cliffs in Medicinal Chemistry : Miniperspective

Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 1.85 MB

english, 2012

22

Activity Landscapes, Information Theory, and Structure - Activity Relationships

Iyer, Preeti, Stumpfe, Dagmar, Vogt, Martin, Bajorath, J., Maggiora, G. M.

Journal:

Molecular Informatics

Year:

2013

Language:

english

File:

PDF, 854 KB

english, 2013

23

Compound Pathway Model To Capture SAR Progression: Comparison of Activity Cliff-Dependent and -Independent Pathways

Stumpfe, Dagmar, Dimova, Dilyana, Heikamp, Kathrin, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 821 KB

english, 2013

24

Do Medicinal Chemists Learn from Activity Cliffs? A Systematic Evaluation of Cliff Progression in Evolving Compound Data Sets

Dimova, Dilyana, Heikamp, Kathrin, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2013

Language:

english

File:

PDF, 971 KB

english, 2013

25

Molecular Mechanism-Based Network-like Similarity Graphs Reveal Relationships between Different Types of Receptor Ligands and Structural Changes that Determine Agonistic, Inverse-Agonistic, and Antagonistic Effects

Iyer, Preeti, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2011

Language:

english

File:

PDF, 3.85 MB

english, 2011

26

Virtual compound screening in drug discovery

Stumpfe, Dagmar, Ripphausen, Peter, Bajorath, Jürgen

Journal:

Future Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 1.27 MB

english, 2012

27

Assessing the Confidence Level of Public Domain Compound Activity Data and the Impact of Alternative Potency Measurements on SAR Analysis

Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2011

Language:

english

File:

PDF, 3.19 MB

english, 2011

28

Development of a Method To Consistently Quantify the Structural Distance between Scaffolds and To Assess Scaffold Hopping Potential

Li, Ruifang, Stumpfe, Dagmar, Vogt, Martin, Geppert, Hanna, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2011

Language:

english

File:

PDF, 1.30 MB

english, 2011

29

Quantifying the Fingerprint Descriptor Dependence of Structure–Activity Relationship Information on a Large Scale

Dimova, Dilyana, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 548 KB

english, 2013

30

Recent Progress in Understanding Activity Cliffs and Their Utility in Medicinal Chemistry

Stumpfe, Dagmar, Hu, Ye, Dimova, Dilyana, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 992 KB

english, 2014

31

New chemotypes for wALADin1-like inhibitors of delta-aminolevulinic acid dehydratase from Wolbachia endobacteria

Lentz, Christian S., Stumpfe, Dagmar, Bajorath, Juergen, Famulok, Michael, Hoerauf, Achim, Pfarr, Kenneth M.

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2013

Language:

english

File:

PDF, 919 KB

english, 2013

32

MMP-Cliffs: Systematic Identification of Activity Cliffs on the Basis of Matched Molecular Pairs

Hu, Xiaoying, Hu, Ye, Vogt, Martin, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 3.18 MB

english, 2012

33

Activity Cliff Networks for Medicinal Chemistry

Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Drug Development Research

Year:

2014

Language:

english

File:

PDF, 436 KB

english, 2014

34

Composition and Topology of Activity Cliff Clusters Formed by Bioactive Compounds

Stumpfe, Dagmar, Dimova, Dilyana, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 2.21 MB

english, 2014

35

A Homogeneous Fluorescence Resonance Energy Transfer System for Monitoring the Activation of a Protein Switch in Real Time

Bill, Anke, Blockus, Heike, Stumpfe, Dagmar, Bajorath, Jürgen, Schmitz, Anton, Famulok, Michael

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 2.36 MB

english, 2011

36

Targeting Multifunctional Proteins by Virtual Screening: Structurally Diverse Cytohesin Inhibitors with Differentiated Biological Functions

Stumpfe, Dagmar, Bill, Anke, Novak, Nina, Loch, Gerrit, Blockus, Heike, Geppert, Hanna, Becker, Thomas, Schmitz, Anton, Hoch, Michael, Kolanus, Waldemar, Famulok, Michael, Bajorath, Jürgen

Journal:

ACS Chemical Biology

Year:

2010

Language:

english

File:

PDF, 1.98 MB

english, 2010

37

Scaffold Hopping Using Two-Dimensional Fingerprints: True Potential, Black Magic, or a Hopeless Endeavor? Guidelines for Virtual Screening

Vogt, Martin, Stumpfe, Dagmar, Geppert, Hanna, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2010

Language:

english

File:

PDF, 4.30 MB

english, 2010

38

Ligand Prediction from Protein Sequence and Small Molecule Information Using Support Vector Machines and Fingerprint Descriptors

Geppert, Hanna, Humrich, Jens, Stumpfe, Dagmar, Gärtner, Thomas, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 4.08 MB

english, 2009

39

Method for the Evaluation of Structure–Activity Relationship Information Associated with Coordinated Activity Cliffs

Dimova, Dilyana, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 4.61 MB

english, 2014

40

Molecular Formal Concept Analysis for Compound Selectivity Profiling in Biologically Annotated Databases

Lounkine, Eugen, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 2.77 MB

english, 2009

41

Specific chemical changes leading to consistent potency increases in structurally diverse active compounds

Dimova, Dilyana, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Year:

2014

Language:

english

File:

PDF, 789 KB

english, 2014

42

Systematic assessment of coordinated activity cliffs formed by kinase inhibitors and detailed characterization of activity cliff clusters and associated SAR information

Dimova, Dilyana, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

European Journal of Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 4.44 MB

english, 2015

43

Visualization of Activity Landscapes and Chemogenomics Data

Hu, Ye, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Molecular Informatics

Year:

2013

Language:

english

File:

PDF, 2.47 MB

english, 2013

44

Computational Polypharmacology Analysis of the Heat Shock Protein 90 Interactome

Anighoro, Andrew, Stumpfe, Dagmar, Heikamp, Kathrin, Beebe, Kristin, Neckers, Leonard M., Bajorath, Jürgen, Rastelli, Giulio

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 1.53 MB

english, 2015

45

Activity cliff clusters as a source of structure–activity relationship information

Dimova, Dilyana, Stumpfe, Dagmar, Hu, Ye, Bajorath, Jürgen

Journal:

Expert Opinion on Drug Discovery

Year:

2015

Language:

english

File:

PDF, 634 KB

english, 2015

46

Structural diversity and potency range distribution of scaffolds from compounds active against current pharmaceutical targets

Kayastha, Shilva, Dimova, Dilyana, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Future Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 1.34 MB

english, 2015

47

Systematic assessment of scaffold hopping versus activity cliff formation across bioactive compound classes following a molecular hierarchy

Stumpfe, Dagmar, Dimova, Dilyana, Bajorath, Jürgen

Journal:

Bioorganic & Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 608 KB

english, 2015

48

Monitoring global growth of activity cliff information over time and assessing activity cliff frequencies and distributions

Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Future Medicinal Chemistry

Year:

2015

Language:

english

File:

PDF, 1.44 MB

english, 2015

49

Systematic assessment of analog relationships between bioactive compounds and promiscuity of analog sets

Dimova, Dilyana, Stumpfe, Dagmar, Bajorath, Jürgen

Journal:

Year:

2016

Language:

english

File:

PDF, 2.16 MB

english, 2016

50

Lessons learned from the design of chemical space networks and opportunities for new applications

Vogt, Martin, Stumpfe, Dagmar, Maggiora, Gerald M., Bajorath, Jürgen

Journal:

Journal of Computer-Aided Molecular Design

Year:

2016

Language:

english

File:

PDF, 5.38 MB

english, 2016