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1

From in silico target prediction to multi-target drug design: Current databases, methods and applications

Alexios Koutsoukas, Benjamin Simms, Johannes Kirchmair, Peter J. Bond, Alan V. Whitmore, Steven Zimmer, Malcolm P. Young, Jeremy L. Jenkins, Meir Glick, Robert C. Glen, Andreas Bender

Journal:

Journal of Proteomics

Year:

2011

Language:

english

File:

PDF, 1.29 MB

english, 2011

2

How Similar Are Similarity Searching Methods? A Principal Component Analysis of Molecular Descriptor Space

Bender, Andreas, Jenkins, Jeremy L., Scheiber, Josef, Sukuru, Sai Chetan K., Glick, Meir, Davies, John W.

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 1.14 MB

english, 2009

3

Novel drug targets in 2018

Ursu, Oleg, Glick, Meir, Oprea, Tudor

Journal:

Nature Reviews Drug Discovery

Year:

2019

Language:

english

File:

PDF, 634 KB

english, 2019

4

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

5

Public Domain HTS Fingerprints: Design and Evaluation of Compound Bioactivity Profiles from PubChem’s Bioassay Repository

Helal, Kazi Yasin, Maciejewski, Mateusz, Gregori-Puigjané, Elisabet, Glick, Meir, Wassermann, Anne Mai

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 1.53 MB

english, 2016

6

REDUCED PETAL PIGMENTATION IN LISIANTHUS (EUSTOMA GRANDIFLORUM) FLOWERS UNDER LOW LIGHT CONDITIONS IS ASSOCIATED WITH DECREASED EXPRESSION OF ANTHOCYANIN BIOSYNTHESIS GENES

Meir, S., Kochanek, B., Glick, A., Salim, S., Lers, A., Burd, S., Philosoph-Hadas, S., Weiss, D.

Journal:

Acta Horticulturae

Year:

2010

Language:

english

File:

PDF, 1007 KB

english, 2010

7

METHYL JASMONATE ENHANCES COLOR AND CAROTENOID CONTENT OF YELLOW-PIGMENTED CUT ROSE FLOWERS

Glick, A., Philosoph-Hadas, S., Vainstein, A., Meir, A., Tadmor, Y., Meir, S.

Journal:

Acta Horticulturae

Year:

2007

Language:

english

File:

PDF, 980 KB

english, 2007

8

CHEMGENIE: integration of chemogenomics data for applications in chemical biology

Kutchukian, Peter S., Chang, Charlie, Fox, Sean J., Cook, Erica, Barnard, Richard, Tellers, David, Wang, Huijun, Pertusi, Dante, Glick, Meir, Sheridan, Robert P., Wallace, Iain, Wassermann, Anne Mai

Journal:

Drug Discovery Today

Year:

2017

Language:

english

File:

PDF, 2.09 MB

english, 2017

9

Novel drug targets in 2018

Ursu, Oleg, Glick, Meir, Oprea, Tudor

Journal:

Nature Reviews Drug Discovery

Year:

2019

File:

PDF, 634 KB

2019

10

A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays

Meir Glick, Amiram Goldblum

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 286 KB

english, 2000

11

Application of Machine Learning to Improve the Results of High-Throughput Docking Against the HIV-1 Protease.

Anthony E. Klon, Meir Glick, John W. Davies

Journal:

Year:

2005

File:

PDF, 9 KB

2005

12

Cover Picture: Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off-Target Effects from Chemical Structure (ChemMedChem 6/2007)

Andreas Bender, Josef Scheiber, Meir Glick, John W. Davies, Kamal Azzaoui, Jacques Hamon, Laszlo Urban, Steven Whitebread, Jeremy L. Jenkins

Journal:

Year:

2007

File:

PDF, 28 KB

2007

13

Enhanced immunogenicity of CTL antigens through mutation of the CD8 binding MHC class I invariant region

Linda Wooldridge, Anna Lissina, Jonathan Vernazza, Emma Gostick, Bruno Laugel, Sarah L. Hutchinson, Fareed Mirza, P. Rod Dunbar, Jonathan M. Boulter, Meir Glick, Vincenzo Cerundolo, Hugo A. van den Be

Journal:

European Journal of Immunology

Year:

2007

Language:

english

File:

PDF, 516 KB

english, 2007

14

Pattern recognition and massively distributed computing

E. Keith Davies, Meir Glick, Karl N. Harrison, W. Graham Richards

Journal:

Journal of Computational Chemistry

Year:

2002

Language:

english

File:

PDF, 1.32 MB

english, 2002

15

Streamlining lead discovery by aligning in silico and high-throughput screening

John W Davies, Meir Glick, Jeremy L Jenkins

Journal:

Current Opinion in Chemical Biology

Year:

2006

Language:

english

File:

PDF, 404 KB

english, 2006

16

The role of computational methods in the identification of bioactive compounds

Meir Glick, Edgar Jacoby

Journal:

Current Opinion in Chemical Biology

Year:

2011

Language:

english

File:

PDF, 250 KB

english, 2011

17

Symptomatic Hypocalcemia Precipitated by Small-Volume Blood Transfusion

Mark J Niven, Meir Zohar, Zvi Shimoni, Joseph Glick

Journal:

Annals of Emergency Medicine

Year:

1998

Language:

english

File:

PDF, 25 KB

english, 1998

18

Computational design and crystal structure of an enhanced affinity mutant human CD8 αα coreceptor

David K. Cole, Pierre J. Rizkallah, Jonathan M. Boulter, Malkit Sami, Anne-lise Vuidepot, Meir Glick, Feng Gao, John I. Bell, Bent K. Jakobsen, George F. Gao

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2007

Language:

english

File:

PDF, 656 KB

english, 2007

19

SPREAD—exploiting chemical features that cause differential activity behavior

Josef Scheiber, Jeremy L. Jenkins, Andreas Bender, Mariusz Milik, Dmitri Mikhailov, Sai Chetan K. Sukuru, Ben Cornett, Steven Whitebread, Laszlo Urban, John W. Davies, Meir Glick

Journal:

Statistical Analysis and Data Mining

Year:

2009

Language:

english

File:

PDF, 453 KB

english, 2009

20

Determining proton positions in an enzyme-inhibitor complex is a first step for theoretical mechanistic studies of aspartic proteinases

Amiram Goldblum, Meir Glick, Anwar Rayan

Journal:

Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta)

Year:

1993

Language:

english

File:

PDF, 1.02 MB

english, 1993

21

Flexible 3D pharmacophores as descriptors of dynamic biological space

James H. Nettles, Jeremy L. Jenkins, Chris Williams, Alex M. Clark, Andreas Bender, Zhan Deng, John W. Davies, Meir Glick

Journal:

Journal of Molecular Graphics and Modelling

Year:

2007

Language:

english

File:

PDF, 1.48 MB

english, 2007

22

Pinpointing anthrax-toxin inhibitors

Glick, Meir, Grant, Guy H., Richards, W. Graham

Journal:

Nature Biotechnology

Year:

2002

Language:

english

File:

PDF, 1.02 MB

english, 2002

23

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

24

A 3D Similarity Method for Scaffold Hopping from Known Drugs or Natural Ligands to New Chemotypes

Jenkins, Jeremy L., Glick, Meir, Davies, John W.

Journal:

Journal of Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 689 KB

english, 2004

25

Prediction of Biological Targets for Compounds Using Multiple-Category Bayesian Models Trained on Chemogenomics Databases

Nidhi,, Glick, Meir, Davies, John W., Jenkins, Jeremy L.

Journal:

Journal of Chemical Information and Modeling

Year:

2006

Language:

english

File:

PDF, 385 KB

english, 2006

26

Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off-Target Effects from Chemical Structure

Andreas Bender, Josef Scheiber, Meir Glick, John W. Davies, Kamal Azzaoui, Jacques Hamon, Laszlo Urban, Steven Whitebread, Jeremy L. Jenkins

Journal:

Year:

2007

Language:

english

File:

PDF, 1.14 MB

english, 2007

27

Prioritization of high throughput screening data of compound mixtures using molecular similarity

GLICK, MEIR, KLON, ANTHONY E., ACKLIN, PIERRE, DAVIES, JOHN W.

Journal:

Molecular Physics

Year:

2003

Language:

english

File:

PDF, 397 KB

english, 2003

28

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

29

Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results

Klon, Anthony E., Glick, Meir, Thoma, Mathis, Acklin, Pierre, Davies, John W.

Journal:

Journal of Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 299 KB

english, 2004

30

Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis

Scheiber, Josef, Chen, Bin, Milik, Mariusz, Sukuru, Sai Chetan K., Bender, Andreas, Mikhailov, Dmitri, Whitebread, Steven, Hamon, Jacques, Azzaoui, Kamal, Urban, Laszlo, Glick, Meir, Davies, John W.,

Journal:

Journal of Chemical Information and Modeling

Year:

2009

Language:

english

File:

PDF, 339 KB

english, 2009

31

Mapping Adverse Drug Reactions in Chemical Space

Scheiber, Josef, Jenkins, Jeremy L., Sukuru, Sai Chetan K., Bender, Andreas, Mikhailov, Dmitri, Milik, Mariusz, Azzaoui, Kamal, Whitebread, Steven, Hamon, Jacques, Urban, Laszlo, Glick, Meir, Davies,

Journal:

Journal of Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 297 KB

english, 2009

32

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

33

Bridging Chemical and Biological Space: “Target Fishing” Using 2D and 3D Molecular Descriptors

Nettles, James H., Jenkins, Jeremy L., Bender, Andreas, Deng, Zhan, Davies, John W., Glick, Meir

Journal:

Journal of Medicinal Chemistry

Year:

2006

Language:

english

File:

PDF, 371 KB

english, 2006

34

“Bayes Affinity Fingerprints” Improve Retrieval Rates in Virtual Screening and Define Orthogonal Bioactivity Space: When Are Multitarget Drugs a Feasible Concept?

Bender, Andreas, Jenkins, Jeremy L., Glick, Meir, Deng, Zhan, Nettles, James H., Davies, John W.

Journal:

Journal of Chemical Information and Modeling

Year:

2006

Language:

english

File:

PDF, 290 KB

english, 2006

35

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

36

“Virtual Fragment Linking”: An Approach To Identify Potent Binders from Low Affinity Fragment Hits

Crisman, Thomas J., Bender, Andreas, Milik, Mariusz, Jenkins, Jeremy L., Scheiber, Josef, Sukuru, Sai Chetan K., Fejzo, Jasna, Hommel, Ulrich, Davies, John W., Glick, Meir

Journal:

Journal of Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 372 KB

english, 2008

37

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

38

Enrichment of High-Throughput Screening Data with Increasing Levels of Noise Using Support Vector Machines, Recursive Partitioning, and Laplacian-Modified Naive Bayesian Classifiers

Glick, Meir, Jenkins, Jeremy L., Nettles, James H., Hitchings, Hamilton, Davies, John W.

Journal:

Journal of Chemical Information and Modeling

Year:

2006

Language:

english

File:

PDF, 265 KB

english, 2006

39

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

40

Identification of Ligand Binding Sites on Proteins Using a Multi-Scale Approach

Glick, Meir, Robinson, Daniel D., Grant, Guy H., Richards, W. Graham

Journal:

Journal of the American Chemical Society

Year:

2002

Language:

english

File:

PDF, 583 KB

english, 2002

41

Extending crystallographic information with semiempirical quantum mechanics and molecular mechanics: A case of aspartic proteinases

Goldblum, Amiram, Rayan, Anwar, Fliess, Amit, Glick, Meir

Journal:

Journal of Chemical Information and Modeling

Year:

1993

Language:

english

File:

PDF, 1.04 MB

english, 1993

42

Understanding False Positives in Reporter Gene Assays: in Silico Chemogenomics Approaches To Prioritize Cell-Based HTS Data

Crisman, Thomas J., Parker, Christian N., Jenkins, Jeremy L., Scheiber, Josef, Thoma, Mathis, Kang, Zhao Bin, Kim, Richard, Bender, Andreas, Nettles, James H., Davies, John W., Glick, Meir

Journal:

Journal of Chemical Information and Modeling

Year:

2007

Language:

english

File:

PDF, 438 KB

english, 2007

43

Use of Ligand Based Models for Protein Domains To Predict Novel Molecular Targets and Applications To Triage Affinity Chromatography Data

Bender, Andreas, Mikhailov, Dmitri, Glick, Meir, Scheiber, Josef, Davies, John W., Cleaver, Stephen, Marshall, Stephen, Tallarico, John A., Harrington, Edmund, Cornella-Taracido, Ivan, Jenkins, Jeremy

Journal:

Journal of Proteome Research

Year:

2009

Language:

english

File:

PDF, 1.26 MB

english, 2009

44

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

45

Docking of Flexible Molecules Using Multiscale Ligand Representations

Glick, Meir, Grant, Guy H., Richards, W. Graham

Journal:

Journal of Medicinal Chemistry

Year:

2002

Language:

english

File:

PDF, 399 KB

english, 2002

46

Combination of a Naive Bayes Classifier with Consensus Scoring Improves Enrichment of High-Throughput Docking Results

Klon, Anthony E., Glick, Meir, Davies, John W.

Journal:

Journal of Medicinal Chemistry

Year:

2004

Language:

english

File:

PDF, 169 KB

english, 2004

47

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

48

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

49

Potent, Selective, and Orally Bioavailable Inhibitors of VPS34 Provide Chemical Tools to Modulate Autophagy in Vivo

Honda, Ayako, Harrington, Edmund, Cornella-Taracido, Ivan, Furet, Pascal, Knapp, Mark S., Glick, Meir, Triantafellow, Ellen, Dowdle, William E., Wiedershain, Dmitri, Maniara, Wieslawa, Moore, Christin

Journal:

ACS Medicinal Chemistry Letters

Year:

2015

Language:

english

File:

PDF, 1.92 MB

english, 2015

50

Construction of a 3D-shaped, natural product like fragment library by fragmentation and diversification of natural products

Prescher, Horst, Koch, Guido, Schuhmann, Tim, Ertl, Peter, Bussenault, Alex, Glick, Meir, Dix, Ina, Petersen, Frank, Lizos, Dimitrios E.

Journal:

Bioorganic & Medicinal Chemistry

Year:

2017

Language:

english

File:

PDF, 1.11 MB

english, 2017