Publications
Computational advances in discovering cryptic pockets for drug discovery
Bemelmans MP, Cournia Z, Damm-Ganamet KL, Gervasio FL, Pande V
Curr Op Struct Biol 2025, Vol. 90 102975
doi: 10.1016/j.sbi.2024.102975
Using deep learning and large protein language models to predict protein-membrane interfaces of peripheral membrane proteins
Paranou S, Chatzigoulas A, Cournia Z.
Bioinformatics Advances, 2024, 4(1), vbae078
doi: 10.1093/bioadv/vbae078
Free energy landscape of the PI3Kα C-terminal activation
Kotzampasi DM, Papadourakis M, Burke JE, Cournia Z.
Comput Struct Biotechnol J. 2024, 23:3118-3131.
doi: 10.1016/j.csbj.2024.07.010
Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators
Diakogiannaki I, Papadourakis M, Spyridaki V, Cournia Z, Koutselos A.
J Chem Inf Model. 2024, 64(13):5140-5150
doi: 10.1021/acs.jcim.3c01195
Editorial: Machine Learning in Materials Science
Merz KM, Choong YS, Cournia Z, Isayev O, Soares TA, Wei GW, Zhu F.
J Chem Inf Model. 2024, 64(10):3959-3960
doi: 10.1021/acs.jcim.4c00727
Applications of Free-Energy Calculations to Biomolecular Processes. A Collection.
Cournia Z, Chipot C.
J Phys Chem B. 2024, 128(14):3299-3301
doi: 10.1021/acs.jpcb.4c01283
Machine learning approaches in predicting allosteric sites
Nerín-Fonz F, Cournia Z.
Curr Opin Struct Biol. 2024, 85:102774
doi: 10.1016/j.sbi.2024.102774
A Perspective on the Prospective Use of AI in Protein Structure Prediction
Versini R, Sritharan S, Aykac Fas B, Tubiana T, Aimeur SZ, Henri J, Erard M, Nüsse O, Andreani J, Baaden M, Fuchs P, Galochkina T, Chatzigoulas A, Cournia Z, Santuz H, Sacquin-Mora S, Taly A.
J Chem Inf Model. 2024, 64(1):26-41
doi: 10.1021/acs.jcim.3c01361
Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications
Koukos PI, Dehghani-Ghahnaviyeh S, Velez-Vega C, Manchester J, Tieleman DP, Duca JS, Souza PCT, Cournia Z
J Chem Theory Comput. 2023, 19(23):8901-8918
doi: 10.1021/acs.jctc.3c00604
Alchemical Free Energy Calculations on Membrane-Associated Proteins
Papadourakis M, Sinenka H, Matricon P, Hénin J, Brannigan G, Pérez-Benito L, Pande V, van Vlijmen H, de Graaf C, Deflorian F, Tresadern G, Cecchini M, Cournia Z
J Chem Theory Comput. 2023, 19(21):7437-7458
doi: 10.1021/acs.jctc.3c00365
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications
Soares TA, Cournia Z, Naidoo K, Amaro R, Wahab H, Merz KM Jr.
J Chem Inf Model. 2023, 63(11):3227-3229
doi: 10.1021/acs.jcim.3c00599
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry
Cournia Z, Soares TA, Wahab HA, Amaro RE
J Chem Inf Model. 2022, 62(24):6287-6291
doi: 10.1021/acs.jcim.2c01543
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design
Chatzigoulas A, Cournia Z
Bioinformatics. 2022, 38(24):5449-5451
doi: 10.1093/bioinformatics/btac680
The orchestrated signaling by PI3Kα and PTEN at the membrane interface
Kotzampasi DK, Premeti K,Papafotika A, Syropoulou V, Christoforidis S, Cournia Z, Leondaritis G
Comput Struct Biotech J. 2022, 20:5607-5621
doi: 10.1016/j.csbj.2022.10.007
Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin
Vakali V, Papadourakis M, Georgiou N, Zoupanos N, Diamantis D, Javornik U , Papakyriakopoulou P, Plavec J, Valsami G, Tzakos A, Tzeli D, Cournia Z, Mavromoustakos T
Molecules. 2022, 27(17), 5490
doi: 10.3390/molecules27175490
Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering.
Christoforou E, Leontiadou H, Noé F, Samios J, Emiris IZ, Cournia Z.
J Chem Theory Comput. 2022, 18(9):5636-5648
doi: 10.1021/acs.jctc.1c00881
Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning
Chatzigoulas A, Cournia Z
Brief Bioinform 2022, bbab518.
doi: 10.1093/bib/bbab518
Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability
Andreadelis I, Kiriakidi S, Lamprakis C, Theodoropoulou A, Doerr S, Chatzigoulas A, Manchester J, Velez-Vega C, Duca J. S., Cournia Z
J Phys Chem B, 2022, 26(7):1504-1519
DOI: 10.1021/acs.jpcb.1c01184
Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations
Makurat S, Cournia Z, Rak J
J Chem Inf Model 2021, 62, 1, 142–149
https://doi.org/10.1021/acs.jcim.1c01157
Free Energy Methods in Drug Discovery—Introduction
Cournia Z, Chipot C, Roux B, York DM, Sherman W. Free Energy Methods in Drug Discovery: Current State and Future Directions, In: "Free Energy Methods in Drug Discovery", ACS Symposium Series #1397, Eds. Armacost KA and Thompson DC, 2021
https://10.1021/bk-2021-1397.ch001
Advancing Women in Chemistry
Cournia Z, Soares TA, Wahab HA, Amaro RE.
J Chem Inf Model. 2021, 61(11):5305-5306.
https://10.1021/acs.jcim.1c01185
The effect of S427F mutation on RXRα activity depends on its dimeric partner
Galdadas I, Bonis V, Vgenopoulou P, Papadourakis M, Kakoulidis P, Stergiou G, Cournia Z, Klinakis A
Chemical Science 2021, 12(44):14700-14710.
https://doi.org/10.1039/D1SC04465F
N-terminal domain mutations of the spike protein are structurally implicated in epitope recognition in emerging SARS-CoV-2 strains
Klinakis A, Cournia Z, Rampias T
Comput Struct Biotechnol J 2021, 19:5556-5567.
https://doi.org/10.1016/j.csbj.2021.10.004
Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines
Pickering B et al
Open Research Europe, 1:1-69
DOI: 10.12688/OPENRESEUROPE.13369.1
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations
Zavitsanou S, Tsengenes A, Papadourakis M, Amendola G, Chatzigoulas A, Dellis D, Cosconati S, Cournia Z.
J Chem Inf Model. 2021, 61(9):4131-4138
https://doi.org/10.1021/acs.jcim.1c00215
Rational Design of Allosteric Modulators: Challenges and Successes
Chatzigoulas A, Cournia Z.
WIREs Computational Molecular Science, 2021, 11(6):e1529
https://doi.org/10.1002/wcms.1529
free preprint in Zenodo
Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments
Lamprakis C, Andreadelis I, Manchester J, Velez-Vega C, Duca JS, Cournia Z.
J Chem Theory Comput. 2021 May 11;17(5):3088-3102
https://doi.org/10.1021/acs.jctc.0c00507
free preprint here: https://pubs.acs.org/articlesonrequest/AOR-EMXPIH7FPZHYTG9DUUSC
Interplay of cholesterol, membrane bilayers and the AT1R: A cholesterol consensus motif on AT1R is revealed
Kiriakidi S, Chatzigiannis C, Papaemmanouil C, Tzakos AG, Cournia Z, Mavromoustakos T
Comput Struct Biotechnol J 2021, 19:110-120
https://doi.org/10.1016/j.csbj.2020.11.042
Editorial: Advances in computational molecular biophysics
Jerome B, Bondar A-N, Cournia Z, Parks JM, Petridis L, Roux B
BBA Gen Subj 2021, 1865(6):129888
DOI: 10.1016/J.BBAGEN.2021.129888
Editorial: Method and Data Sharing and Reproducibility of Scientific Results
Merz KM, Jr, Rommie A, Cournia Z, Rarey M, Soares T, Tropsha A, Wahab HA, Wang R
J Chem Inf Model 2021, 60, 12, 5868–5869
DOI: 10.1021/ACS.JCIM.0C01389
Fostering global data sharing: highlighting the recommendations of the Research Data Alliance COVID-19 Working Group
Austin C et al, Wellcome Open Res. 2020, 5:267
https://doi.org/10.12688/wellcomeopenres.16378.1
Coating of magnetic nanoparticles affects their interactions with model cell membranes.
Lazaratos M, Karathanou K, Mainas L, Chatzigoulas A, Pippa N, Demetzos C, Cournia Z.
Biochim Biophys Acta Gen Subj. 2020, 1864(11):129671
https://doi.org/10.1016/j.bbagen.2020.129671
Rigorous free energy simulations in virtual screening
Cournia Z, Allen BK, Beuming T, Pearlman DA, Radak BK, Sherman W
J Chem Inf Model, 2020, Epub ahead of print
https://doi.org/10.1021/acs.jcim.0c00116
Allostery in Membrane Proteins
Cournia Z and Chatzigoulas A
Curr Op Struct Biol, 2020, 62, 197-204
https://doi.org/10.1016/j.sbi.2020.03.006
Unravelling the effect of the E545K mutation on PI3Kα kinase
Galdadas I, Gervasio, FL, Cournia Z
Chem Sci, 2020, 11, 3511-3515
https://doi.org/10.1039/C9SC05903B
The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations
Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, Mobley DL, Chodera JD.
J Comput Aided Mol Des, 2020, 34, 601–633
http://dx.doi.org/10.1007/s10822-020-00290-5
For the free BioRxiv version click here.
Novel Directions in Free Energy Methods and Applications
Armacost K, Riniker S, Cournia Z
J Chem Inf Model, 2020 60(1):1-5
http://dx.doi.org/10.1021/acs.jcim.9b01174
ChemBioServer2.0: An Advanced Web Server for Filtering, Clustering and Networking of Chemical Compounds Facilitating Both Drug Discovery and Repurposing
Karatzas E, Zamora JE, Athanasiadis E, Dellis D, Cournia Z, Spyrou G
Bioinformatics 2020, pii: btz976
http://dx.doi.org/10.1093/bioinformatics/btz976
for a free version read the article in ChemRXiv
Compounds for use in treating or preventing cancerous diseases
Stellas D, Tamvakopoulos C, Klinakis A, Efstratiadis A, Cournia Z
US Patent 2019 10,287,294B2
Phase Diagram of a Stratum Corneum Lipid Mixture.
Podewitz M, Wang Y, Gkeka P, von Grafenstein S, Liedl KR, Cournia Z.
J Phys Chem B. 2018, 122(46):10505-10521
http://dx.doi.org/10.1021/acs.jpcb.8b07200
Nano-Crystal: A web-based crystallographic tool for the construction of nanoparticles based on their crystal habit.
Chatzigoulas A, Karathanou K, Dellis D, Cournia Z*
J Chem Inf Model, 2018, 58(12):2380-2386
http://dx.doi.org/10.1021/acs.jcim.8b00269
Read the Free preprint on ChemRxiv
Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations.
Leontiadou H, Galdadas I, Athanasiou C, Cournia Z*
Sci Rep, 2018, 8(1):15544.
http://dx.doi.org/10.1038/s41598-018-27044-6
Women in Computational Chemistry
Wahab HA, Amaro RE, Cournia Z
J Chem Inf Model 2018, 58(11):2175-2177.
https://pubs.acs.org/doi/10.1021/acs.jcim.8b00642
Effect of 5-trans Isomer of Arachidonic Acid on Model Liposomal Membranes Studied by a Combined Simulation and Experimental Approach
Tremi I, Anagnostopoulos D, Spyratou E, Gkeka P, Georgakilas AG*, Chatgilialoglu C*, Cournia Z*
J Memb Biol 2018, 251(3), 475-489
https://doi.org/10.1007/s00232-018-0029-8
Read the Free preprint on BioRxiv
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 C, Vasilakaki S, Dellis D, Cournia Z*
J Comput Aid Mol Des, 2018, 32(1):21-44.
DOWNLOAD the article here!
DOWNLOAD the SI here!
http://dx.doi.org/10.1007/s10822-017-0075-9
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
Cournia Z*, Allen B, Sherman W*
J Chem Inf Model 2017, 57(12):2911-2937.
http://10.1021/acs.jcim.7b00564 (Open Access)
Multiscale simulations reveal IRMOF-74-III as a potent drug carrier for gemcitabine delivery
Kotzabasaki M, Galdadas I, Tylianakis E, Klontza E, Cournia Z*, Froudakis G*.
J Mater Chem B, 2017, 5, 3277-3282
http://dx.doi.org/10.1039/C7TB00220C
Magnetic nanoparticles coated with polyarabic acid demonstrate enhanced drug delivery and imaging properties for cancer theranostic applications.
Patitsa M, Karathanou K, Kanaki Z, Tzioga L, Pippa N, Demetzos C, Verganelakis DA, Cournia Z*, Klinakis A*.
Sci Rep. 2017, 7, 1, pp. 775-777
http://dx.doi.org/10.1038/s41598-017-00836-y
Nurr1:RXRα heterodimer activation as monotherapy for Parkinson’s disease
Spathis AD, Asvos X, Ziavra D, Karampelas T, Topouzis S, Cournia Z, Qing X, Alexakos P, Smits LM, Dalla C, Rideout HJ, Schwamborn JC, Tamvakopoulos C, Fokas D, Vassilatis DK.
Proc Natl Acad Sci U S A 2017, 114, 15, pp. 3999-4004
http://dx.doi.org/10.1073/pnas.1616874114
Self-assembly of anionic, ligand-coated nanoparticles in lipid membranes
Angelikopoulos P, Sarkisov L, Cournia Z, Gkeka P.
Nanoscale. 2017, 9, pp. 1040-1048
http://dx.doi.org/10.1039/C6NR05853A
Pyrazole-based potent inhibitors of GGT1: Synthesis, biological evaluation, and molecular docking studies
Mansha M, Kumari UU, Cournia Z, Ullah N.
Eur J Med Chem. 2016, 124, pp. 666-676
http://dx.doi.org/10.1016/j.ejmech.2016.09.002
DPPC-cholesterol phase diagram using coarse-grained MD simulations
Wang Y, Gkeka P, Fuchs JE, Liedl, KR, Cournia Z*.
BBA Biomembranes. 2016, 1858(11), pp. 2846-2857
http://dx.doi.org/10.1016/j.bbamem.2016.08.005
Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM
Ioannidis H, Drakopoulos A, Tzitzoglaki C, Homeyer N, Kolarov F, Gkeka P, Freudenberger K, Liolios C, Gauglitz G, Cournia Z*, Gohlke H*, Kolocouris A*.
J Chem Inf Model. 2016, 56(5), pp. 862-876
http://dx.doi.org/10.1021/acs.jcim.6b00079
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, 248(4), pp. 611-640.
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.
Download Free PDF
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://dx.doi.org/10.1016/j.bbamem.2013.12.012
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, 9 (2), pp 1272–1281.
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, 28(22), pp. 3002-3.
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, 7(7):1286-94.
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, 20(19):5811-4.
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, 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, 111(7):1786-801.
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, (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
Find here the program documentation
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
NANO-Crystal WebServer
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