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1

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry

Mazzolari, Angelica, Nunes-Alves, Ariane, Wahab, Habibah A., Amaro, Rommie E., Cournia, Zoe, Merz, Kenneth M.

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 1.01 MB

2020

2

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations

Cournia, Zoe, Allen, Bryce, Sherman, Woody

Journal:

Journal of Chemical Information and Modeling

Year:

2017

Language:

english

File:

PDF, 5.60 MB

english, 2017

3

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances

Lionta, Evanthia, Spyrou, George, Vassilatis, Demetrios, Cournia, Zoe

Journal:

Current Topics in Medicinal Chemistry

Year:

2014

Language:

english

File:

PDF, 546 KB

english, 2014

4

Exploring Novel Directions in Free Energy Calculations

Armacost, Kira A., Riniker, Sereina, Cournia, Zoe

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 552 KB

2020

5

Force-Field Development and Molecular Dynamics Simulations of Ferrocene–Peptide Conjugates as a Scaffold for Hydrogenase Mimics

Xavier de Hatten, Zoe Cournia, Ivan Huc, Jeremy C. Smith, Nils Metzler-Nolte

Journal:

Chemistry - A European Journal

Year:

2007

Language:

english

File:

PDF, 832 KB

english, 2007

6

A molecular mechanics force field for biologically important sterols

Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann

Journal:

Journal of Computational Chemistry

Year:

2005

Language:

english

File:

PDF, 478 KB

english, 2005

7

Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF)

Alissa A. Hare, Lin Leng, Sunilkumar Gandavadi, Xin Du, Zoe Cournia, Richard Bucala, William L. Jorgensen

Journal:

Bioorganic & Medicinal Chemistry Letters

Year:

2010

Language:

english

File:

PDF, 436 KB

english, 2010

8

AFMM: A molecular mechanics force field vibrational parametrization program

A.C. Vaiana, Z. Cournia, I.B. Costescu, J.C. Smith

Journal:

Computer Physics Communications

Year:

2005

Language:

english

File:

PDF, 107 KB

english, 2005

9

3-D eye movement analysis

Andrew Duchowski, Eric Medlin, Nathan Cournia, Hunter Murphy, Anand Gramopadhye, Santosh Nair, Jeenal Vorah, Brian Melloy

Journal:

Behavior Research Methods

Year:

2002

Language:

english

File:

PDF, 1.94 MB

english, 2002

10

Structural Characterization and Computer-Aided Optimization of a Small-Molecule Inhibitor of the Arp2/3 Complex, a Key Regulator of the Actin Cytoskeleton

Andrew W. Baggett, Dr. Zoe Cournia, Min Suk Han, Dr. George Patargias, Dr. Adam C. Glass, Prof. Shih-Yuan Liu, Prof. Brad J. Nolen

Journal:

Year:

2012

Language:

english

File:

PDF, 985 KB

english, 2012

11

Inside Cover: Structural Characterization and Computer-Aided Optimization of a Small-Molecule Inhibitor of the Arp2/3 Complex, a Key Regulator of the Actin Cytoskeleton (ChemMedChem 7/2012)

Andrew W. Baggett, Dr. Zoe Cournia, Min Suk Han, Dr. George Patargias, Dr. Adam C. Glass, Prof. Shih-Yuan Liu, Prof. Brad J. Nolen

Journal:

Year:

2012

File:

PDF, 891 KB

2012

12

Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore

Gkeka, Paraskevi, Eleftheratos, Stelios, Kolocouris, Antonios, Cournia, Zoe

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 4.04 MB

english, 2013

13

[IEEE 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) - Larnaca, Cyprus (2012.11.11-2012.11.13)] 2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) - Enhancing the effectiveness of virtual screening by using the ChemBioServer: Application to the discovery of PI3Kα inhibitors

Gkeka, Paraskevi, Athanasiadis, Emmanouil, Spyrou, George, Cournia, Zoe

Year:

2012

Language:

english

File:

PDF, 383 KB

english, 2012

14

Allosteric Modulation of WT and H1047R Mutant PI3Kα Investigated by MD Simulations

Gkeka, Paraskevi, Evangelidis, Thomas, Cournia, Zoe

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 40 KB

english, 2013

15

Study of Nanoparticle-Lipid Bilayer Interactions: Insights from Coarse-Grained Molecular Dynamics Simulations

Gkeka, Paraskevi, Angelikopoulos, Panagiotis, Cournia, Zoe

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 39 KB

english, 2013

16

[ACM Press CHI '03 extended abstracts - Ft. Lauderdale, Florida, USA (2003.04.05-2003.04.10)] CHI '03 extended abstracts on Human factors in computing systems - CHI '03 - Gaze- vs. hand-based pointing in virtual environments

Cournia, Nathan, Smith, John D., Duchowski, Andrew T.

Year:

2003

Language:

english

File:

PDF, 232 KB

english, 2003

17

Insights into the molecular basis of action of the AT1 antagonist losartan using a combined NMR spectroscopy and computational approach

Zervou, Maria, Cournia, Zoe, Potamitis, Constantinos, Patargias, George, Durdagi, Serdar, Grdadolnik, Simona Golic, Mavromoustakos, Thomas

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2014

Language:

english

File:

PDF, 2.85 MB

english, 2014

18

Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine Membrane: A Molecular Dynamics Simulation Study

Cournia, Zoe, Ullmann, G. Matthias, Smith, Jeremy C.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 850 KB

english, 2007

19

Discovery of Human Macrophage Migration Inhibitory Factor (MIF)-CD74 Antagonists via Virtual Screening

Cournia, Zoe, Leng, Lin, Gandavadi, Sunilkumar, Du, Xin, Bucala, Richard, Jorgensen, William L.

Journal:

Journal of Medicinal Chemistry

Year:

2009

Language:

english

File:

PDF, 1011 KB

english, 2009

20

Therapeutic Effects of an Anti-Myc Drug on Mouse Pancreatic Cancer

Stellas, D., Szabolcs, M., Koul, S., Li, Z., Polyzos, A., Anagnostopoulos, C., Cournia, Z., Tamvakopoulos, C., Klinakis, A., Efstratiadis, A.

Journal:

JNCI Journal of the National Cancer Institute

Year:

2014

Language:

english

File:

PDF, 1.38 MB

english, 2014

21

Gaze-Contingent Displays: A Review

Duchowski, Andrew T., Cournia, Nathan, Murphy, Hunter

Journal:

CyberPsychology & Behavior

Year:

2004

Language:

english

File:

PDF, 432 KB

english, 2004

22

Exploring a Non-ATP Pocket for Potential Allosteric Modulation of PI3Kα

Gkeka, Paraskevi, Papafotika, Alexandra, Christoforidis, Savvas, Cournia, Zoe

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 5.33 MB

english, 2015

23

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Cournia, Zoe, Allen, Toby W., Andricioaei, Ioan, Antonny, Bruno, Baum, Daniel, Brannigan, Grace, Buchete, Nicolae-Viorel, Deckman, Jason T., Delemotte, Lucie, del Val, Coral, Friedman, Ran, Gkeka, Par

Journal:

Journal of Membrane Biology

Year:

2015

Language:

english

File:

PDF, 3.91 MB

english, 2015

24

ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery

Athanasiadis, E., Cournia, Z., Spyrou, G.

Journal:

Year:

2012

Language:

english

File:

PDF, 88 KB

english, 2012

25

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant

Gkeka, Paraskevi, Evangelidis, Thomas, Pavlaki, Maria, Lazani, Vasiliki, Christoforidis, Savvas, Agianian, Bogos, Cournia, Zoe, de Groot, Bert L.

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.43 MB

english, 2014

26

Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion

Gkeka, Paraskevi, Angelikopoulos, Panagiotis, Sarkisov, Lev, Cournia, Zoe, Grubmüller, Helmut

Journal:

PLoS Computational Biology

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

27

[ACM Press the 44th annual southeast regional conference - Melbourne, Florida (2006.03.10-2006.03.12)] Proceedings of the 44th annual southeast regional conference on - ACM-SE 44 - Chessboard domination on programmable graphics hardware

Cournia, Nathan

Year:

2006

Language:

english

File:

PDF, 203 KB

english, 2006

28

[ACM Press ACM SIGGRAPH 2012 Posters - Los Angeles, California (2012.08.05-2012.08.09)] ACM SIGGRAPH 2012 Posters on - SIGGRAPH '12 - Crom

Cournia, Nathan, Smith, Bradley, Spitzak, Bill, Vanover, Casey, Rijpkema, Hans, Tomlinson, Josh, Litke, Nathan

Year:

2012

Language:

english

File:

PDF, 166 KB

english, 2012

29

Derivation of a molecular mechanics force field for cholesterol

Cournia, Zoe, Vaiana, A. C., Ullmann, G. M., Smith, J. C.

Journal:

Pure & Applied Chemistry

Year:

2004

Language:

english

File:

PDF, 248 KB

english, 2004

30

[ACM Press the Eye tracking research & applications symposium - San Antonio, Texas (2004.03.22-2004.03.24)] Proceedings of the Eye tracking research & applications symposium on Eye tracking research & applications - ETRA'2004 - Visual deictic reference in a collaborative virtual environment

Duchowski, Andrew T., Cournia, Nathan, Cumming, Brian, McCallum, Daniel, Gramopadhye, Anand, Greenstein, Joel, Sadasivan, Sajay, Tyrrell, Richard A.

Year:

2004

Language:

english

File:

PDF, 2.30 MB

english, 2004

31

Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM

Ioannidis, Harris, Drakopoulos, Antonios, Tzitzoglaki, Christina, Homeyer, Nadine, Kolarov, Felix, Gkeka, Paraskevi, Freudenberger, Kathrin-Maria, Liolios, Christos C., Gauglitz, Guenter, Cournia, Zoe

Journal:

Journal of Chemical Information and Modeling

Year:

2016

Language:

english

File:

PDF, 1.84 MB

english, 2016

32

[ACM Press the symposium - New Orleans, Louisiana (2002.03.25-2002.03.27)] Proceedings of the symposium on Eye tracking research & applications - ETRA '02 - 3D eye movement analysis for VR visual inspection training

Duchowski, Andrew T., Medlin, Eric, Cournia, Nathan, Gramopadhye, Anand, Melloy, Brian, Nair, Santosh

Year:

2002

Language:

english

File:

PDF, 1024 KB

english, 2002

33

DPPC-cholesterol phase diagram using coarse-grained MD simulations

Wang, Yin, Gkeka, Paraskevi, Fuchs, Julian E., Liedl, Klaus R., Cournia, Zoe

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2016

Language:

english

File:

PDF, 2.70 MB

english, 2016

34

Human aldehyde dehydrogenase 7A1 (ALDH7A1) expression affects cancer cell proliferation, migration and cell protection against oxidative stress

Elsalem, L., Fotopoulos, A., Papathanasiou, A., Allison, S., Moreb, J., Cournia, Z., Pors, K.

Journal:

European Journal of Cancer

Year:

2016

Language:

english

File:

PDF, 60 KB

english, 2016

35

Self-assembly of anionic, ligand-coated nanoparticles in lipid membranes

Angelikopoulos, Panagiotis, Sarkisov, Lev, Cournia, Zoe, Gkeka, Paraskevi

Journal:

Year:

2016

Language:

english

File:

PDF, 8.56 MB

english, 2016

36

Nurr1:RXRα heterodimer activation as monotherapy for Parkinson’s disease

Spathis, Athanasios D., Asvos, Xenophon, Ziavra, Despina, Karampelas, Theodoros, Topouzis, Stavros, Cournia, Zoe, Qing, Xiaobing, Alexakos, Pavlos, Smits, Lisa M., Dalla, Christina, Rideout, Hardy J.,

Journal:

Proceedings of the National Academy of Sciences

Year:

2017

Language:

english

File:

PDF, 1.70 MB

english, 2017

37

Multiscale simulations reveal IRMOF-74-III as a potent drug carrier for gemcitabine delivery

Kotzabasaki, Marianna, Galdadas, Ioannis, Tylianakis, Emmanuel, Klontzas, Emmanuel, Cournia, Zoe, Froudakis, George E.

Journal:

Journal of Materials Chemistry B

Year:

2017

Language:

english

File:

PDF, 1.72 MB

english, 2017

38

Magnetic nanoparticles coated with polyarabic acid demonstrate enhanced drug delivery and imaging properties for cancer theranostic applications

Patitsa, Maria, Karathanou, Konstantina, Kanaki, Zoi, Tzioga, Lamprini, Pippa, Natassa, Demetzos, Constantinos, Verganelakis, Dimitris A., Cournia, Zoe, Klinakis, Apostolos

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.74 MB

english, 2017

39

Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

Athanasiou, Christina, Vasilakaki, Sofia, Dellis, Dimitris, Cournia, Zoe

Journal:

Journal of Computer-Aided Molecular Design

Year:

2017

Language:

english

File:

PDF, 3.87 MB

english, 2017

40

Effect of 5-trans Isomer of Arachidonic Acid on Model Liposomal Membranes Studied by a Combined Simulation and Experimental Approach

Tremi, Ioanna, Anagnostopoulos, Dimitrios, Spyratou, Ellas, Gkeka, Paraskevi, Georgakilas, Alexandros G., Chatgilialoglu, Chryssostomos, Cournia, Zoe

Journal:

Journal of Membrane Biology

Year:

2018

Language:

english

File:

PDF, 3.60 MB

english, 2018

41

In This Issue, Volume 9, Issue 9

Journal:

ACS Medicinal Chemistry Letters

Year:

2018

Language:

english

File:

PDF, 954 KB

english, 2018

42

Women in Computational Chemistry

Wahab, Habibah A, Amaro, Rommie E., Cournia, Zoe

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 294 KB

english, 2018

43

NanoCrystal: A web-based crystallographic tool for the construction of nanoparticles based on their crystal habit

Chatzigoulas, Alexios, Karathanou, Konstantina, Dellis, Dimitris, Cournia, Zoe

Journal:

Journal of Chemical Information and Modeling

Year:

2018

Language:

english

File:

PDF, 1.38 MB

english, 2018

44

The Phase Diagram of a Stratum Corneum Lipid Mixture

Podewitz, Maren, Wang, Yin, Gkeka, Paraskevi, von Grafenstein, Susanne, Liedl, Klaus R., Cournia, Zoe

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 2.01 MB

english, 2018

45

Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations

Leontiadou, Hari, Galdadas, Ioannis, Athanasiou, Christina, Cournia, Zoe

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 6.25 MB

english, 2018

46

Correction to “NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit”

Chatzigoulas, Alexios, Karathanou, Konstantina, Dellis, Dimitris, Cournia, Zoe

Journal:

Journal of Chemical Information and Modeling

Year:

2019

File:

PDF, 174 KB

2019

47

A Celebration of Women in Computational Chemistry

Wahab, Habibah A., Amaro, Rommie E., Cournia, Zoe

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 370 KB

english, 2019

48

ChemBioServer 2.0: An advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing

Karatzas, Evangelos, Zamora, Juan Eiros, Athanasiadis, Emmanouil, Dellis, Dimitris, Cournia, Zoe, Spyrou, George M, Cowen, Lenore

Journal:

Year:

2020

File:

PDF, 190 KB

2020

49

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Rizzi, Andrea, Jensen, Travis, Slochower, David R., Aldeghi, Matteo, Gapsys, Vytautas, Ntekoumes, Dimitris, Bosisio, Stefano, Papadourakis, Michail, Henriksen, Niel M., de Groot, Bert L., Cournia, Zoe

Journal:

Journal of Computer-Aided Molecular Design

Year:

2020

File:

PDF, 4.04 MB

2020

50

Novel Directions in Free Energy Methods and Applications

Armacost, Kira A., Riniker, Sereina, Cournia, Zoe

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 322 KB

2020

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