BRFAA - Biomedical Research Foundation Academy Of Athens
Biomedical Research Foundation Academy Of AthensAcademy Of Athens

Publications

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.
Cournia Z, Allen TW, Andricioaei I, Antonny B, Baum D, Brannigan G, Buchete NV, Deckman JT, Delemotte L, Del Val C, Friedman R, Gkeka P, Hege HC, Hénin J, Kasimova MA, Kolocouris A, Klein ML, Khalid S, Lemieux MJ, Lindow N, Roy M, Selent J, Tarek M, Tofoleanu F, Vanni S, Urban S, Wales DJ, Smith JC, Bondar AN.
J Membr Biol. 2015 Aug;248(4):611-40.
http://dx.doi.org/10.1007/s00232-015-9802-0

Exploring a Non-ATP Pocket for Potential Allosteric Modulation of PI3Kα.
Gkeka P, Papafotika A, Christoforidis S, Cournia Z.
J Phys Chem B. 2015, 119 (3), pp. 1002-1016.
http://dx.doi.org/10.1021/jp506423e

Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion
Gkeka, P, Angelikopoulos P, Sarkisov L, Cournia Z.
PLoS Comput Biol. 2014, 10 (10):e1003917
http://dx.doi.org/10.1371/journal.pcbi.1003917

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant.
Gkeka P, Evangelidis T, Pavlaki M, Lazani V, Christoforidis S, Agianian B, Cournia Z.
PLoS Comput Biol. 2014, 10 (10):e1003895.
http://dx.doi.org/10.1371/journal.pcbi.1003895

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.
J Natl Cancer Inst. 2014, 106 (12), pii: dju320.
http://dx.doi.org/10.1093/jnci/dju320

Structure-Based Virtual Screening for Drug Discovery: Principles, Applications and Recent Advances
Lionta E, Spyrou G, Vassilatis D, Cournia Z
Curr Top Med Chem, 2014, 14 (16), pp. 1923-1938.
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http://dx.doi.org/10.2174/1568026614666140929124445

Insights into the Molecular Basis of Action of the AT1 Antagonist Losartan Using a Combined NMR Spectroscopy and Computational Approach
Zervou M, Cournia Z, Potamitis C, Patargias G, Durdagi S, Golic Grdadolnik S, Mavromoustakos T
Biochim Biophys Acta. 2014, 1838 (3), pp. 1031–1046.
http://www.sciencedirect.com/science/article/pii/S0005273613004513

Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore.
Gkeka P, Eleftheratos S, Kolocouris A, Cournia Z.
J Chem Theor Comp. 2013 Epub ahead of print
http://dx.doi.org/10.1021/ct300899n

ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery. 
Athanasiadis E, Cournia Z, Spyrou G.
Bioinformatics. 2012 Nov 15;28(22):3002-3. Epub 2012 Sep 8.
http://dx.doi.org/10.1093/bioinformatics/bts551

Structural characterization and computer-aided optimization of a small-molecule inhibitor of the Arp2/3 complex, a key regulator of the actin cytoskeleton.
Baggett AW, Cournia Z, Han MS, Patargias G, Glass AC, Liu SY, Nolen BJ.
ChemMedChem. 2012 Jul;7(7):1286-94. Epub 2012 May 23.
http://dx.doi.org/10.1002/cmdc.201200104

Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF).
Hare AA, Leng L, Gandavadi S, Du X, Cournia Z, Bucala R, Jorgensen WL.
Bioorg Med Chem Lett. 2010 Oct 1;20(19):5811-4. Epub 2010 Aug 3.
http://dx.doi.org/10.1016/j.bmcl.2010.07.129

Discovery of human macrophage migration inhibitory factor (MIF)-CD74 antagonists via virtual screening.
Cournia Z, Leng L, Gandavadi S, Du X, Bucala R, Jorgensen WL.
J Med Chem. 2009 Jan 22;52(2):416-24.
http://dx.doi.org/10.1021/jm801100v

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.
de Hatten X, Cournia Z, Huc I, Smith JC, Metzler-Nolte
N. Chemistry. 2007;13(29):8139-52.
http://dx.doi.org/10.1002/chem.200700358

Differential effects of cholesterol, ergosterol and lanosterol on a dipalmitoyl phosphatidylcholine membrane: a molecular dynamics simulation study.
Cournia Z, Ullmann GM, Smith JC.
J Phys Chem B. 2007 Feb 22;111(7):1786-801. Epub 2007 Jan 30.
http://dx.doi.org/10.1021/jp065172i

A molecular mechanics force field for biologically important sterols.
Cournia Z, Smith JC, Ullmann GM
J Comput Chem. 2005 Oct;26(13):1383-99.
http://dx.doi.org/10.1002/jcc.20277

AFMM: A molecular mechanics force-field vibrational parametrization program.
Vaiana AC, Cournia Z, Costescu IB, Smith JC
Comput. Phys. Commun 2005, 167:34-42.
http://dx.doi.org/10.1016/j.cpc.2004.12.005

Derivation of a Molecular Mechanics Force-Field for Cholesterol.
Cournia Z, Vaiana AC, Smith JC, Ullmann GM
Pure Appl. Chem. 2004, 76:189-196.
http://dx.doi.org/10.1351/pac200476010189