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1

Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs

Harger, Matthew, Li, Daniel, Wang, Zhi, Dalby, Kevin, Lagardère, Louis, Piquemal, Jean-Philip, Ponder, Jay, Ren, Pengyu

Journal:

Journal of Computational Chemistry

Year:

2017

Language:

english

File:

PDF, 635 KB

english, 2017

2

Corrigendum to “Purification and characterization of tagless recombinant human elongation factor 2 kinase (eEF-2K) expressed in Escherichia coli” [Protein Expression and Purification 79 (2011) 237–244]

Abramczyk, Olga, Tavares, Clint D.J., Devkota, Ashwini K., Ryazanov, Alexey G., Turk, Benjamin E., Riggs, Austen F., Ozpolat, Bulent, Dalby, Kevin N.

Journal:

Protein Expression and Purification

Year:

2012

Language:

english

File:

PDF, 125 KB

english, 2012

3

Identification and Validation of Novel PERK Inhibitors

Wang, Qiantao, Park, Jihyun, Devkota, Ashwini K., Cho, Eun Jeong, Dalby, Kevin N., Ren, Pengyu

Journal:

Journal of Chemical Information and Modeling

Year:

2014

Language:

english

File:

PDF, 5.66 MB

english, 2014

4

Design, synthesis and biological evaluation of fused naphthofuro[3,2-c] quinoline-6,7,12-triones and pyrano[3,2-c]quinoline-6,7,8,13-tetraones derivatives as ERK inhibitors with efficacy in BRAF-mutant melanoma

Aly, Ashraf A., El-Sheref, Essmat M., Bakheet, Momtaz E.M., Mourad, Mai A.E., Bräse, Stefan, Ibrahim, Mahmoud A.A., Nieger, Martin, Garvalov, Boyan K., Dalby, Kevin N., Kaoud, Tamer S.

Journal:

Bioorganic Chemistry

Year:

2019

Language:

english

File:

PDF, 4.39 MB

english, 2019

5

Reaction Mechanisms. Part 1. Polar Reactions

Journal:

Year:

2003

File:

PDF, 55 KB

2003

6

Reaction Mechanisms. Part 2. Polar Reactions

Journal:

Year:

2004

File:

PDF, 49 KB

2004

7

Reaction Mechanisms. Part 2. Polar Reactions

Journal:

Year:

2005

File:

PDF, 8 KB

2005

8

A kinetic approach towards understanding substrate interactions and the catalytic mechanism of the serine/threonine protein kinase ERK2: identifying a potential regulatory role for divalent magnesium

William F Waas, Mark A Rainey, Anna E Szafranska, Kari Cox, Kevin N Dalby

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2004

Language:

english

File:

PDF, 355 KB

english, 2004

9

Quantifying ERK2–protein interactions by fluorescence anisotropy: PEA-15 inhibits ERK2 by blocking the binding of DEJL domains

Kari Callaway, Mark A. Rainey, Kevin N. Dalby

Journal:

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

Year:

2005

Language:

english

File:

PDF, 270 KB

english, 2005

10

Following in vitro activation of mitogen-activated protein kinases by mass spectrometry and tryptic peptide analysis: purifying fully activated p38 mitogen-activated protein kinase α

Anna E. Szafranska, Xuemei Luo, Kevin N. Dalby

Journal:

Analytical Biochemistry

Year:

2005

Language:

english

File:

PDF, 643 KB

english, 2005

11

Synthesis and biological evaluation of p38α kinase-targeting dialkynylimidazoles

Jing Li, Tamer S. Kaoud, Christophe Laroche, Kevin N. Dalby, Sean M. Kerwin

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2009

Language:

english

File:

PDF, 642 KB

english, 2009

12

Conformational preference of ChaK1 binding peptides: a molecular dynamics study

Jiajing Zhang, Christopher A King, Kevin Dalby, Pengyu Ren

Journal:

Year:

2010

Language:

english

File:

PDF, 2.38 MB

english, 2010

13

193-nm photodissociation of singly and multiply charged peptide anions for acidic proteome characterization

James A. Madsen, Tamer S. Kaoud, Kevin N. Dalby, Jennifer S. Brodbelt

Journal:

Year:

2011

Language:

english

File:

PDF, 298 KB

english, 2011

14

Phage display identifies novel peptides that bind extracellular-regulated protein kinase 2 to compete with transcription factor binding

Mark A. Rainey, Klaus D. Linse, Kevin N. Dalby

Journal:

Journal of Physical Organic Chemistry

Year:

2004

Language:

english

File:

PDF, 173 KB

english, 2004

15

Virtual screening using molecular simulations

Tianyi Yang, Johnny C. Wu, Chunli Yan, Yuanfeng Wang, Ray Luo, Michael B. Gonzales, Kevin N. Dalby, Pengyu Ren

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2011

Language:

english

File:

PDF, 521 KB

english, 2011

16

Dopamine depletion and subsequent treatment with l-DOPA, but not the long-lived dopamine agonist pergolide, enhances activity of the Akt pathway in the rat striatum

Evgeny Bychkov, M. Rafiuddin Ahmed, Kevin N. Dalby, Eugenia V. Gurevich

Journal:

Journal of Neurochemistry

Year:

2007

Language:

english

File:

PDF, 956 KB

english, 2007

17

Kinetic mechanism for p38 MAP kinase α : A partial rapid-equilibrium random-order ternary-complex mechanism for the phosphorylation of a protein substrate

Anna E. Szafranska, Kevin N. Dalby

Journal:

Year:

2005

Language:

english

File:

PDF, 407 KB

english, 2005

18

Investigating the Kinetic Mechanism of Inhibition of Elongation Factor 2 Kinase by NH125: Evidence of a Common in Vitro Artifact

Devkota, Ashwini K., Tavares, Clint D. J., Warthaka, Mangalika, Abramczyk, Olga, Marshall, Kyle D., Kaoud, Tamer S., Gorgulu, Kivanc, Ozpolat, Bulent, Dalby, Kevin N.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.52 MB

english, 2012

19

Charge-Site-Dependent Dissociation of Hydrogen-Rich Radical Peptide Cations upon Vacuum UV Photoexcitation

Dr. James A. Madsen, Ryan R. Cheng, Tamer S. Kaoud, Prof. Kevin N. Dalby, Prof. Dmitrii E. Makarov, Prof. Jennifer S. Brodbelt

Journal:

Chemistry - A European Journal

Year:

2012

Language:

english

File:

PDF, 976 KB

english, 2012

20

Purification of a Model Substrate for Transcription Factor Phosphorylation by ERK2

William F. Waas, Kevin N. Dalby

Journal:

Protein Expression and Purification

Year:

2001

Language:

english

File:

PDF, 163 KB

english, 2001

21

The cyanobacterial toxin microcystin binds covalently to cysteine-273 on protein phosphatase 1

Robert W. MacKintosh, Kevin N. Dalby, David G. Campbell, Patricia T.W. Cohen, Philip Cohen, Carol MacKintosh

Journal:

Year:

1995

Language:

english

File:

PDF, 563 KB

english, 1995

22

Comparison of the specificities of p70 S6 kinase and MAPKAP kinase-1 identifies a relatively specific substrate for p70 S6 kinase: the N-terminal kinase domain of MAPKAP kinase-1 is essential for peptide phosphorylation

Ian A. Leighton, Kevin N. Dalby, F. Barry Caudwell, Patricia T.W. Cohen, Philip Cohen

Journal:

Year:

1995

Language:

english

File:

PDF, 742 KB

english, 1995

23

Regulation of protein phosphorylation within the MKK1–ERK2 complex by MP1 and the MP1•P14 heterodimer

Amrita Brahma, Kevin N. Dalby

Journal:

Archives of Biochemistry and Biophysics

Year:

2007

Language:

english

File:

PDF, 494 KB

english, 2007

24

The expression and purification of the N-terminal activation domain of the transcription factor c-Myc: A model substrate for exploring ERK2 docking interactions

William F. Waas, Kevin N. Dalby

Journal:

Protein Expression and Purification

Year:

2007

Language:

english

File:

PDF, 241 KB

english, 2007

25

Purification and characterization of tagless recombinant human elongation factor 2 kinase (eEF-2K) expressed in Escherichia coli

Olga Abramczyk, Clint D.J. Tavares, Ashwini K. Devkota, Alexey G. Ryazanov, Benjamin E. Turk, Austen F. Riggs, Bulent Ozpolat, Kevin N. Dalby

Journal:

Protein Expression and Purification

Year:

2011

Language:

english

File:

PDF, 583 KB

english, 2011

26

Conserved Elements of the Cytochrome P-450 Superfamily Found in Monoamine Oxidase B

Duane A Lewis, Kevin N Dalby, Creed W Abell

Journal:

NeuroToxicology

Year:

2004

Language:

english

File:

PDF, 156 KB

english, 2004

27

Manipulating JNK Signaling with (−)-Zuonin A

Kaoud, Tamer S., Park, Heekwang, Mitra, Shreya, Yan, Chunli, Tseng, Chun-Chia, Shi, Yue, Jose, Jiney, Taliaferro, Juliana M., Lee, Kiyoun, Ren, Pengyu, Hong, Jiyong, Dalby, Kevin N.

Journal:

ACS Chemical Biology

Year:

2012

Language:

english

File:

PDF, 1.66 MB

english, 2012

28

A Fluorescence-Based Assay for p38α Recruitment Site Binders: Identification of Rooperol as a Novel p38α Kinase Inhibitor

Li, Jing, Kaoud, Tamer S., LeVieux, Jake, Gilbreath, Brad, Moharana, Swapna, Dalby, Kevin N., Kerwin, Sean M.

Journal:

Year:

2013

Language:

english

File:

PDF, 950 KB

english, 2013

29

Lifetimes of Imidinium Ions in Aqueous Solution

Dalby, Kevin N., Jencks, William P.

Journal:

Journal of the American Chemical Society

Year:

1997

Language:

english

File:

PDF, 246 KB

english, 1997

30

Physiological Concentrations of Divalent Magnesium Ion Activate the Serine/Threonine Specific Protein Kinase ERK2 †

Waas, William F., Dalby, Kevin N.

Journal:

Year:

2003

Language:

english

File:

PDF, 177 KB

english, 2003

31

Understanding the Specificity of a Docking Interaction between JNK1 and the Scaffolding Protein JIP1

Yan, Chunli, Kaoud, Tamer, Lee, Sunbae, Dalby, Kevin N., Ren, Pengyu

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 5.54 MB

english, 2011

32

Toward a Stable Hydroxyphosphorane

Hanes, Robert E., Lynch, Vincent M., Anslyn, Eric V., Dalby, Kevin N.

Journal:

Organic Letters

Year:

2002

Language:

english

File:

PDF, 60 KB

english, 2002

33

General acid catalysis of the reversible addition of thiolate anions to cyanamide

Dalby, Kevin N., Jencks, William P.

Journal:

Journal of the Chemical Society Perkin Transactions 2

Year:

1997

Language:

english

File:

PDF, 129 KB

english, 1997

34

Seasonal variation in Eurasian WigeonAnas penelopesex and age ratios from hunter-based surveys

Kevin Kuhlmann Clausen, Lars Dalby, Peter Sunde, Thomas Kjær Christensen, Bjarke Egelund, Anthony David Fox

Journal:

Journal of Ornithology

Year:

2013

Language:

english

File:

PDF, 296 KB

english, 2013

35

10 Reaction mechanisms : Part (ii) Polar reactions

Dalby, Kevin N.

Journal:

Annual Reports Section "B" (Organic Chemistry)

Year:

2003

Language:

english

File:

PDF, 317 KB

english, 2003

36

In-Situ Generation of Differential Sensors that Fingerprint Kinases and the Cellular Response to Their Expression

Zamora-Olivares, Diana, Kaoud, Tamer S., Dalby, Kevin N., Anslyn, Eric V.

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 1.31 MB

english, 2013

37

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

Mu, Xiaojiao, Wang, Qiantao, Wang, Lee-Ping, Fried, Stephen D., Piquemal, Jean-Philip, Dalby, Kevin N., Ren, Pengyu

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 1.42 MB

english, 2014

38

Effect of preventive primary care outreach on health related quality of life among older adults at risk of functional decline: randomised controlled trial

Jenny Ploeg, Kevin Brazil, Brian Hutchison, Janusz Kaczorowski, Dawn M Dalby, Charles H Goldsmith and William Furlong

Journal:

Year:

2010

Language:

english

File:

PDF, 344 KB

english, 2010

39

Elucidating binding modes of zuonin A enantiomers to JNK1 via in silico methods

Dykstra, Daniel W., Dalby, Kevin N., Ren, Pengyu

Journal:

Journal of Molecular Graphics and Modelling

Year:

2013

Language:

english

File:

PDF, 1.31 MB

english, 2013

40

Properties and Regulation of a Transiently Assembled ERK2·Ets-1 Signaling Complex †

Callaway, Kari A., Rainey, Mark A., Riggs, Austen F., Abramczyk, Olga, Dalby, Kevin N.

Journal:

Year:

2006

Language:

english

File:

PDF, 713 KB

english, 2006

41

The Anti-Apoptotic Protein PEA-15 Is a Tight Binding Inhibitor of ERK1 and ERK2, Which Blocks Docking Interactions at the D-Recruitment Site †

Callaway, Kari, Abramczyk, Olga, Martin, Lance, Dalby, Kevin N.

Journal:

Year:

2007

Language:

english

File:

PDF, 540 KB

english, 2007

42

Docking Interactions of Hematopoietic Tyrosine Phosphatase with MAP Kinases ERK2 and p38α

Piserchio, Andrea, Francis, Dana M., Koveal, Dorothy, Dalby, Kevin N., Page, Rebecca, Peti, Wolfgang, Ghose, Ranajeet

Journal:

Year:

2012

Language:

english

File:

PDF, 896 KB

english, 2012

43

Proximity-Induced Catalysis by the Protein Kinase ERK2

Rainey, Mark A., Callaway, Kari, Barnes, Richard, Wilson, Brian, Dalby, Kevin N.

Journal:

Journal of the American Chemical Society

Year:

2005

Language:

english

File:

PDF, 118 KB

english, 2005

44

Two Rate-Limiting Steps in the Kinetic Mechanism of the Serine/Threonine Specific Protein Kinase ERK2: A Case of Fast Phosphorylation Followed by Fast Product Release †

Waas, William F., Rainey, Mark A., Szafranska, Anna E., Dalby, Kevin N.

Journal:

Year:

2003

Language:

english

File:

PDF, 307 KB

english, 2003

45

Development of JNK2-Selective Peptide Inhibitors That Inhibit Breast Cancer Cell Migration

Kaoud, Tamer S., Mitra, Shreya, Lee, Sunbae, Taliaferro, Juliana, Cantrell, Michael, Linse, Klaus D., Van Den Berg, Carla L., Dalby, Kevin N.

Journal:

ACS Chemical Biology

Year:

2011

Language:

english

File:

PDF, 4.83 MB

english, 2011

46

Nonvisual Arrestins Function as Simple Scaffolds Assembling the MKK4–JNK3α2 Signaling Complex

Zhan, Xuanzhi, Kaoud, Tamer S., Dalby, Kevin N., Gurevich, Vsevolod V.

Journal:

Year:

2011

Language:

english

File:

PDF, 2.38 MB

english, 2011

47

Examining Docking Interactions on ERK2 with Modular Peptide Substrates

Lee, Sunbae, Warthaka, Mangalika, Yan, Chunli, Kaoud, Tamer S, Ren, Pengyu, Dalby, Kevin N.

Journal:

Year:

2011

Language:

english

File:

PDF, 2.68 MB

english, 2011

48

Expanding the Repertoire of an ERK2 Recruitment Site: Cysteine Footprinting Identifies the D-Recruitment Site as a Mediator of Ets-1 Binding †

Abramczyk, Olga, Rainey, Mark A., Barnes, Richard, Martin, Lance, Dalby, Kevin N.

Journal:

Year:

2007

Language:

english

File:

PDF, 927 KB

english, 2007

49

Synthesis and biological evaluation of pyrido[2,3-d]pyrimidine-2,4-dione derivatives as eEF-2K inhibitors

Edupuganti, Ramakrishna, Wang, Qiantao, Tavares, Clint D.J., Chitjian, Catrina A., Bachman, James L., Ren, Pengyu, Anslyn, Eric V., Dalby, Kevin N.

Journal:

Bioorganic & Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 925 KB

english, 2014

50

Phosphorylation of the Transcription Factor Ets-1 by ERK2: Rapid Dissociation of ADP and Phospho-Ets-1

Callaway, Kari, Waas, William F., Rainey, Mark A., Ren, Pengyu, Dalby, Kevin N.

Journal:

Year:

2010

Language:

english

File:

PDF, 3.00 MB

english, 2010