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1

Rethinking Molecular Similarity: Comparing Compounds on the Basis of Biological Activity

Petrone, Paula M., Simms, Benjamin, Nigsch, Florian, Lounkine, Eugen, Kutchukian, Peter, Cornett, Allen, Deng, Zhan, Davies, John W., Jenkins, Jeremy L., Glick, Meir

Journal:

ACS Chemical Biology

Year:

2012

Language:

english

File:

PDF, 4.21 MB

english, 2012

2

Dark chemical matter as a promising starting point for drug lead discovery

Wassermann, Anne Mai, Lounkine, Eugen, Hoepfner, Dominic, Le Goff, Gaelle, King, Frederick J, Studer, Christian, Peltier, John M, Grippo, Melissa L, Prindle, Vivian, Tao, Jianshi, Schuffenhauer, Ansga

Journal:

Nature Chemical Biology

Year:

2015

Language:

english

File:

PDF, 1.95 MB

english, 2015

3

Improving the Search Performance of Extended Connectivity Fingerprints through Activity-Oriented Feature Filtering and Application of a Bit-Density-Dependent Similarity Function

Ye Hu, Eugen Lounkine, Jürgen Bajorath

Journal:

Year:

2009

Language:

english

File:

PDF, 327 KB

english, 2009

4

Fragment Formal Concept Analysis Accurately Classifies Compounds with Closely Related Biological Activities

Felix Krüger, Eugen Lounkine, Jürgen Bajorath

Journal:

Year:

2009

Language:

english

File:

PDF, 327 KB

english, 2009

5

Assessment of complex SARs using Formal Concept Analysis of fragment combinations

E Lounkine, J Auer, J Bajorath

Journal:

Chemistry Central Journal

Year:

2009

Language:

english

File:

PDF, 63 KB

english, 2009

6

Adaptation of formal concept analysis for the systematic exploration of structure-activity and structure-selectivity relationships

Eugen Lounkine, Jürgen Bajorath

Journal:

Journal of Cheminformatics

Year:

2010

Language:

english

File:

PDF, 144 KB

english, 2010

7

RelACCS-FP: A Structural Minimalist Approach to Fingerprint Design

Ye Hu, Eugen Lounkine, José Batista, Jürgen Bajorath

Journal:

Chemical Biology & Drug Design

Year:

2008

Language:

english

File:

PDF, 456 KB

english, 2008

8

Filtering and Counting of Extended Connectivity Fingerprint Features Maximizes Compound Recall and the Structural Diversity of Hits

Ye Hu, Eugen Lounkine, Jürgen Bajorath

Journal:

Chemical Biology & Drug Design

Year:

2009

Language:

english

File:

PDF, 411 KB

english, 2009

9

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

10

Large-scale prediction and testing of drug activity on side-effect targets

Lounkine, Eugen, Keiser, Michael J., Whitebread, Steven, Mikhailov, Dmitri, Hamon, Jacques, Jenkins, Jeremy L., Lavan, Paul, Weber, Eckhard, Doak, Allison K., Côté, Serge, Shoichet, Brian K., Urban, L

Journal:

Year:

2012

Language:

english

File:

PDF, 1.26 MB

english, 2012

11

Computational methods for early predictive safety assessment from biological and chemical data

Nigsch, Florian, Lounkine, Eugen, McCarren, Patrick, Cornett, Ben, Glick, Meir, Azzaoui, Kamal, Urban, Laszlo, Marc, Philippe, Müller, Arne, Hahne, Florian

Journal:

Expert Opinion on Drug Metabolism & Toxicology

Year:

2011

Language:

english

File:

PDF, 893 KB

english, 2011

12

Data structures and computational tools for the extraction of SAR information from large compound sets

Mathias Wawer, Eugen Lounkine, Anne M. Wassermann, Jürgen Bajorath

Journal:

Drug Discovery Today

Year:

2010

Language:

english

File:

PDF, 630 KB

english, 2010

13

Systematic Analysis of Public Domain Compound Potency Data Identifies Selective Molecular Scaffolds across Druggable Target Families

Hu, Ye, Wassermann, Anne Mai, Lounkine, Eugen, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2010

Language:

english

File:

PDF, 3.67 MB

english, 2010

14

Chemotography for multi-target SAR analysis in the context of biological pathways

Eugen Lounkine, Peter Kutchukian, Paula Petrone, John W. Davies, Meir Glick

Journal:

Bioorganic & Medicinal Chemistry

Year:

2012

Language:

english

File:

PDF, 1.42 MB

english, 2012

15

Biodiversity of small molecules – a new perspective in screening set selection

Petrone, Paula M., Wassermann, Anne Mai, Lounkine, Eugen, Kutchukian, Peter, Simms, Benjamin, Jenkins, Jeremy, Selzer, Paul, Glick, Meir

Journal:

Drug Discovery Today

Year:

2013

Language:

english

File:

PDF, 554 KB

english, 2013

16

Core Trees and Consensus Fragment Sequences for Molecular Representation and Similarity Analysis

Lounkine, Eugen, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2008

Language:

english

File:

PDF, 266 KB

english, 2008

17

Activity-Aware Clustering of High Throughput Screening Data and Elucidation of Orthogonal Structure–Activity Relationships

Lounkine, Eugen, Nigsch, Florian, Jenkins, Jeremy L., Glick, Meir

Journal:

Journal of Chemical Information and Modeling

Year:

2011

Language:

english

File:

PDF, 1.07 MB

english, 2011

18

SARANEA: A Freely Available Program To Mine Structure−Activity and Structure−Selectivity Relationship Information in Compound Data Sets

Lounkine, Eugen, Wawer, Mathias, Wassermann, Anne Mai, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2010

Language:

english

File:

PDF, 3.38 MB

english, 2010

19

Efficient Search of Chemical Space: Navigating from Fragments to Structurally Diverse Chemotypes

Wassermann, Anne Mai, Kutchukian, Peter S., Lounkine, Eugen, Luethi, Tiffany, Hamon, Jacques, Bocker, Michael T., Malik, Hasnain A., Cowan-Jacob, Sandra W., Glick, Meir

Journal:

Journal of Medicinal Chemistry

Year:

2013

Language:

english

File:

PDF, 2.38 MB

english, 2013

20

Similarity Searching Using Fingerprints of Molecular Fragments Involved in Protein−Ligand Interactions

Tan, Lu, Lounkine, Eugen, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2008

Language:

english

File:

PDF, 1.09 MB

english, 2008

21

Many Approved Drugs Have Bioactive Analogs With Different Target Annotations

Hu, Ye, Lounkine, Eugen, Bajorath, Jürgen

Journal:

The AAPS Journal

Year:

2014

Language:

english

File:

PDF, 1.83 MB

english, 2014

22

A Screening Pattern Recognition Method Finds New and Divergent Targets for Drugs and Natural Products

Wassermann, Anne Mai, Lounkine, Eugen, Urban, Laszlo, Whitebread, Steven, Chen, Shanni, Hughes, Kevin, Guo, Hongqiu, Kutlina, Elena, Fekete, Alexander, Klumpp, Martin, Glick, Meir

Journal:

ACS Chemical Biology

Year:

2014

Language:

english

File:

PDF, 1.80 MB

english, 2014

23

Bioturbo Similarity Searching: Combining Chemical and Biological Similarity To Discover Structurally Diverse Bioactive Molecules

Wassermann, Anne Mai, Lounkine, Eugen, Glick, Meir

Journal:

Journal of Chemical Information and Modeling

Year:

2013

Language:

english

File:

PDF, 1.87 MB

english, 2013

24

Mapping of Activity-Specific Fragment Pathways Isolated from Random Fragment Populations Reveals the Formation of Coherent Molecular Cores

Lounkine, Eugen, Batista, José, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 187 KB

english, 2007

25

Identifying mechanism-of-action targets for drugs and probes

Gregori-Puigjane, E., Setola, V., Hert, J., Crews, B. A., Irwin, J. J., Lounkine, E., Marnett, L., Roth, B. L., Shoichet, B. K.

Journal:

Proceedings of the National Academy of Sciences

Year:

2012

Language:

english

File:

PDF, 632 KB

english, 2012

26

Topological Fragment Index for the Analysis of Molecular Substructures and Their Topological Environment in Active Compounds

Lounkine, Eugen, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 962 KB

english, 2009

27

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

28

Formal Concept Analysis for the Identification of Molecular Fragment Combinations Specific for Active and Highly Potent Compounds

Lounkine, Eugen, Auer, Jens, Bajorath, Jürgen

Journal:

Journal of Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 1.41 MB

english, 2008

29

Translation of off-target effects: prediction of ADRs by integrated experimental and computational approach

Urban, Laszlo, Maciejewski, Mateusz, Lounkine, Eugen, Whitebread, Steven, Jenkins, Jeremy L., Hamon, Jacques, Fekete, Alexander, Muller, Patrick Y.

Journal:

Toxicology Research

Year:

2014

Language:

english

File:

PDF, 3.51 MB

english, 2014

30

The opportunities of mining historical and collective data in drug discovery

Wassermann, Anne Mai, Lounkine, Eugen, Davies, John W., Glick, Meir, Camargo, L. Miguel

Journal:

Drug Discovery Today

Year:

2015

Language:

english

File:

PDF, 1.40 MB

english, 2015

31

Experimental Design Strategy: Weak Reinforcement Leads to Increased Hit Rates and Enhanced Chemical Diversity

Maciejewski, Mateusz, Wassermann, Anne Mai, Glick, Meir, Lounkine, Eugen

Journal:

Journal of Chemical Information and Modeling

Year:

2015

Language:

english

File:

PDF, 1.16 MB

english, 2015

32

Random Molecular Fragment Methods in Computational Medicinal Chemistry

Lounkine, Eugen, Batista, Jose, Bajorath, Jurgen

Journal:

Current Medicinal Chemistry

Year:

2008

File:

PDF, 568 KB

2008

33

Random Molecular Fragment Methods in Computational Medicinal Chemistry

Lounkine, Eugen, Batista, Jose, Bajorath, Jurgen

Journal:

Current Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 568 KB

english, 2008

34

Relevance of Feature Combinations for Similarity Searching Using General or Activity Class-Directed Molecular Fingerprints

Lounkine, Eugen, Hu, Ye, Batista, José, Bajorath, Jürgen

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 895 KB

english, 2009