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Contact details


Zoe  Cournia,  PhD
Investigator - Associate Professor Level
Center for Translational Research
Biomedical Research Foundation
Academy of Athens
​4, Soranou Ephessiou, 11527 Athens
Greece

Telephone :+30 210 6597 195
Fax :+30 210 6597 545
e-mail : zcournia@bioacademy.gr



About us

Our work focuses on exploring structure and dynamics of biological systems and linking those to function using computational methods. Our goal is to utilize this knowledge in order to understand the biophysics behind biomolecules and rationally design new chemical entities that could contribute in treating human disease. For this purpose we employ a wide range of physics-based techniques, such as enhanced sampling Molecular Dynamics, Monte Carlo, quantum mechanics calculations, free energy perturbation simulations, Markov State models, Machine Learning, pharmacological property prediction, docking, and homology/loop modeling.

News

  • January 2023: Zoe will Chair the European Chemical Society Conference on Computational and Theoretical Chemistry, 27-31 August 2023, in Thessaloniki, Greece. Check out the website and register!
  • December 2022: Zoe co-edited the "Advancing Women in Chemistry" special issue of the Journal of Chemical Information and Modeling.
  • December 2022: Our paper "DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design" is out in Bioinformatics.
  • November 2022: Congratulations to Sophia Kiriakidi for receiving the Notara award oof the Academy of Athens for our article on Interplay of cholesterol, membrane bilayers and the AT1R: A cholesterol consensus motif on AT1R is revealed.
  • November 2022: Alexis and Zoe present at the "Beyond alpha fold" workshop in Paris.
  • October 2022: New review article on 'The orchestrated signaling by PI3Kα and PTEN at the membrane interface" in collaboration with the University of Ioannina
  • September 2022: We welcome the new MSc students!
  • August 2022: New article in the Cyclodextrin special issue of Molecules: "Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin" 
  • August 2022: New research on Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering.
  • March 2022: Congratulations to Alexis Chatzigoulas for successfully defending his PhD thesis at the University of Athens!
  • December 2021: Check out our newest publication on The effect of S427F mutation on RXRα activity depends on its dimeric partner.
  • December 2021: Zoe presents two talks in Pacifichem 2021 (virtual)
  • November 2021: Zoe chairs the European Conference on Theoretical and Computational Chemistry - online
  • November 2021: Zoe presents in the SouthEastern European Forum of GEANT on "The added value of EOSC for research"
  • October 2021: We are launching a new Special Issue on "Advancing Women in Chemistry" with JCIM!
  • October 2021: New COVID-19 research - in collaboration with two BRFAA groups.
  • September 2021: Our lab is coordinating the Allostery in Drug  Discovery Innovative Training Network, funded by the European Commission.
  • September 2021: We participate in the NAMD user forum and present FEPrepare. Find the FEPrepare publication here!
  • August 2021: Congratulations to Michalis Papadourakis for winning the Bodossaki Postdoctoral Fellowship!
  • June 2021: Zoe co-organizes the 2021 Workshop on Free Energy Methods in Drug Design.
  • ​May 2021: Zoe co-edited a special issue on computational molecular biophysics in honor of Jeremy C Smith.
  • April 2021: We worked with the COVID-19 RDA group to issue recommendations for data sharing in the COVID-19 era.
  • March 2021: Read our new paper on Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments.
  • January 2021:New research on the Interplay of cholesterol, membrane bilayers and the AT1R published in Comput Struct Biotech J
  • December 2020: We publish an Editorial on Method and Data Sharing and Reproducibility of Scientific Results.
  • November 2020: Editorial on "Exploring Novel Directions in Free Energy Calculations" special issue, published in JCIM
  • October 2020: Read our perspective on the impact of a special issue on Women in Computational Chemistry that we co-edited
  • September 2020: Alexis and Zoe present at the 11th Hellenic Conference on Artificial Intelligence / AINST2020 on the "Prediction of protein-membrane interfaces of peripheral membrane proteins using machine learning"
  • August 2020: Our latest paper is out in BBA Gen Subj on nanoparticle-membrane interactions
  • July 2020: Congratulations to Ioannis Vaxevanakis, PhD student, for winning the Bodossaki scholarship!
  • June 2020: Our perspective on "Rigorous Free Energy Simulations in Virtual Screening" is now the most read of the month in J Chem Inf Model.
  • May 2020: Read our review on Allostery in Membrane Proteins, published in Curr Opin Struct Biol.
  • May 2020: We participated in the SAMPL6 SAMPLing challenge. Read the paper here.
  • April 2020: Welcome to the new project students Katerina, Katerina, Spyros, Ektoras - all trainings will be held online due to the COVID situation.
  • March 2020: Zoe joins the Research Data Alliance COVID-19 Working Group within the OMICS Subgroup and drafted the structural data guidelines/best practices.
  • February 2020: Read our new research findings on PI3Kα in Chemical Science: Unravelling the effect of the E545K mutation on PI3Kα kinase
  • ​February 2020: We organized a mini Symposium for the Human Brain Project CDP6
  • January 2020: Read our editorial for the Special Issue on "Novel Directions in Free Energy Methods and Applications" for the Journal of Chemical Information and Modeling.
  • December 2019: ChemBioServer2 is now ready to use and accepted for publication in Bioinformatics! 
  • November 2019: Participation and Oral presentation in the MolSSI Workshop: "Molecular dynamics software Interoperability", New York USA.
  • October 2019: Zoe co-organizes a Patent workshop in BRFAA.
  • October 2019: Zoe presents our results on Free Energy Perturbation in the Symposium: "From Free Energy Perturbation to Biomedicine: Bridging Experiment and Computation in Chemical Biology" in Shenzhen, China.
  • September 2019: Zoe presents our results in Allostery in Drug Design in the "Computational Advances in Drug Discovery conference, Sestri Levante, Italy.
  • August 2019: PRACE Summer of HPC students Rebecca Lait (UK) and Antonio Miranda (Spain) are hosted in our lab.
  • July 2019: Our lab organized the first Symposium on "Computational methods in drug and materials design" in BRFAA, Greece.
  • June 2019: Our first patent is now granted in the US! 
  • May 2019: Zoe co-organizes the CECAM node workshop: "Challenges in modeling and simulations of nanoparticles in complex environments" in IIT, Genoa, Italy.
  • May 2019: Zoe presents our results on Free Energy Perturbation in the Alchemical Free Energy Workshop 2019.
  • May 2019: Zoe presents lab work on "Allostery in oncogenic protein drug design" at the European Workshop for Drug Design".
  • May 2019: Participation and oral presentation in Euro HPC Summit week and PRACEdays, Poznan Poland.
  • April 2019: Zoe presents two talks at the Spring Meeting of the American Chemical Society, Orlando, USA.
  • March 2019: Zoe speaks in the Webinar "Women at the Interface of Computational Chemistry and Drug Discovery", American Chemical Society.
  • February 2019: Presentation at the PRACE PCT training: "Introduction to Molecular Modelling (materials and bio) and Molecular dynamics in HPC @GRNET"
    January 2019:  Phaedon Brotzakis arrived from ETH Zurich for an HPC Europa 3 fellowship.
  • December 2018: Leandro Battini arrived from the University of Buenos for an HPC Europa 3 fellowship.
  • November 2018: Read our newest research on the stratum corneum (top layer of the epidermis) phase diagram.
  • November 2018: We are offering NANOCRYSTAL a new tool/web-service with which you can construct nanoparticles of any type and any size and use it for modeling studies! Here's the paper and the website.
  • October 2018: Read our newest publication on how the mutant E545K over-activates PI3Kα.
  • October 2018: We welcome a new PhD student Dora, and new diploma thesis students Dimitris, Anastasia.
  • September 2018: Alexis, Matina, Zoe are presenting in the 2018 EuroQSAR conference, Thessaloniki, Greece
  • September 2018: We co-organized the joint BioExcel-VISEEM workshop for Advanced Biomolecular Simulations, Athens, Greece.
  • September 2018: Alexis wins the IKY PhD fellowship
  • August 2018: Matina accepts a PhD position at the University of Oxford, Department of Chemistry.
  • July 2018: The lab welcomes the Summer of HPC students, Petteri Vainikka and Pedro Santos.
  • June 2018: Zoe will be the Vice-Chair of the Gordon Research Conference in Computational Chemistry, Vermont USA.
  • April 2018: Zoe participates in the AACR conference in Chicago, and the lab explains our research in the Athens Science Festival!
  • April 2018: Read our newest publication on the effect of trans fats in healthy membranes!
  • March 2018: Zoe attends the American Chemical Society Spring meeting to present our nanoparticle work, and participate in the Editorial Advisory Board meetings of the ACS Med Chem Letters and the Journal of Chemical Information and Modeling.
  • February 2018: The lab is now part of the Human Brain Project with a grant for modeling allosteric drugs. We join a consortium of > 100 European labs in Europe's 1 Billion Euro flagship program!
  • January 2018: We made it in the cover of JCIM! 
  • December 2017: Our review on Free Energy Perturbation calculations is out! and is selected by the American Chemical Society Publications as an Editor's Choice article (freely available)!
  • November 2017: Our D3R paper is out!
  • November 2017: The lab participates in the 68th Hellenic Conference for Biochemistry and Molecular Biology. Alexis, Christina, Cleopatra, and Matina present their work.
  • October 2017: The lab participates in the 12th Conference of the Hellenic Society for Computational Biology and Bioinformatics and Alexis, Michalis & Lefteris receive an Honorable Mention.
  • September 2017: Our D3R manuscript is accepted and we rank #1 in the competition! Giannis presents his thesis.
  • August 2017: Alexis and Zoe present our research on nanoparticle modeling in the Nanosciences Forum, Mainz, Germany.
  • July 2017: Alexis wins a travel grant award to present his research on building crystal nanoparticles in the Nanoscience Connecting the Disciplines conference, Mainz, Germany. 
  • June 2017: We welcome the Summer Students 2017 in the lab!
  • May 2017: Read our newest publication on using Metal-Organic Frameworks as drug delivery systems.
  • April 2017: The lab participates in a study on discovering novel therapeutics for Parkinson's disease.
  • April 2017: Zoe travels to the American Chemical Society meeting in San Francisco to present our results on modeling Nanoparticle-Membrane interactions.
  • March 2017: The lab ranks in the top 5 teams (together with Eli Lily, Merck, University of Edinburgh, University of Strasburg, National Research Council Canada) in the D3R worldwide computer-aided drug design competition.
  • March 2017: Zoe presents lab results at the International Supercomputing Conference in Mexico 2017.
  • March 2017: Zoe presents lab results at the Hellenic Innovation Forum in Athens.
  • February 2017: Christina defends successfully her diploma thesis at the Chemical Engineering Department of NTUA.
  • February 2017: The lab participates in the "Mind the lab" event inside the Athens metro stations, to promote Science, Technology, Engineering, and Math awareness to the public.
  • January 2017: Giannis is accepted as a PhD student in the lab of Professor Francesco Gervasio in UCL, London. 
  • December 2016: Konstantina successfully presents her Master's thesis at BRFAA.
  • December 2016: The lab participates in the D3R Grand Challenge to predict the crystallographic poses of 36 ligands spanning all chemical series.
  • November 2016: Our latest paper on Self-assembly of anionic, ligand-coated nanoparticles in lipid membranes is published in Nanoscale.
  • October 2016: The lab participates in the Joint International Conference of the Hellenic Crystallographic Association and the Hellenic Society for Computational Biology and Bioinformatics HeCrA-HSCBB16. Anaxagoras, Christina,Youli, Zoe present their research.
  • October 2016: Zoe presents at the Workshop on Targeted Drug Discovery hosted in NHRF, Athens.
  • September 2016: Read our newest publication on Pyrazole-based potent inhibitors of GGT1: Synthesis, biological evaluation, and molecular docking studies
  • September 2016: September is conference month! Zoe presents the lab's results in the EuroQSAR conference in Verona, Italy; the EMLG conference in Chania, Greece; the Schrodinger User Meeting in London, UK; the SLURM conference in Athens, Greece, and the Sanofi Drug Design meeting in Paris, France.
  • August 2016: Read our newest publication on DPPC-cholesterol phase diagram using coarse-grained MD simulations.
  • July 2016: Zoe presents our PI3Ka research to the Gordon Research Conference in Computational Chemistry and is elected as the next co-vice chair for 2018 and co-chair for 2020.
  • July 2016: Congratulations to Marilena for successfully defending her Master's thesis at the Faculty of Pharmacy. Marilena is off to Yale University for her doctoral studies.
  • July 2016: The lab welcomes Samanta and Juan, two students in the Summer of High Performance Computing Program from PRACE.
  • June 2016: Watch here videos from national TV lab appearances.
  • May 2016: Zoe receives the first Ada Lovelace PRACE award in Prague.
  • April 2016: Our newest research on the influenza A virus protein M2 is accepted for publication in J Chem Inf Model
  • March 2016: Zoe attends the ACS National meeting "Computers in Chemistry" in San Diego and presents our newest results on anti-Myc research.
  • February 2016: Zoe attends the "Advances and Progress in Drug Design" conference in London.
  • February 2016: Marilena is accepted to the Chemistry Department, Yale University School of Graduate Studies for her doctoral studies.
  • January 2016: Zoe becomes a member of the J Chem Inf Model Editorial Advisory Board.
  • January 2016: Evi joins Sanofi in Paris with a permament job in the computer-aided drug design R&D department.
  • December 2015: Konstantina is accepted to the group of Prof. A.N. Bondar, Freie Universitaet Berlin for her doctoral studies.
  • November 2015: Konstantina attends the 2nd Workshop on High Throughput Molecular Dynamics in Barcelona, Spain.
  • November 2015: Zoe presents our membrane drug design work in the CECAM workshop "Understanding function of proteins in membrane by atomistic and multiscale simulations" in Lugano, Switzerland.
  • October 2015: Dora wins the first poster prize at the HSCBB2015 conference!
  • October 2015: The lab participates at the HSCBB2015 conference and Dora, Evi, Giannis, Konstantina, Marilena present their work.
  • September 2015: Zoe presents our PI3Kα findings on allosterically modulating H1047R and E545K oncogenic mutants in the CECAM conference "Computational Advances in Drug Discovery".
  • August 2015: Zoe presents our work on nanoparticle-membrane interactions at the 1st Zing Computational Chemical Biology conference.
  • July 2015: Read our latest review on membrane structure and dynamics.
  • June 2015: Marilena wins one of the three poster prizes at the 9th European Joint Meeting for Medicinal Chemistry for her work on Myc.
  • June 2015: The lab participates in the 9th European Joint Meeting for Medicinal Chemistry in Athens, Greece.
  • May 2015: Zoe and Marilena attend the 10th European Conference for Drug Design in Siena, Italy and present our PI3Ka and Myc results. Marilena wins the best poster prize award.
  • April 2015: Evi and Zoe attend the Metadynamics workshop in London, UK
  • April 2015: Zoe presents our PI3Ka results in the Hellenic Oncology Conference in Athens
  • March 2015: Zoe presents two talks at the American Chemical Society Spring meeting, in Denver, USA and two talks at the ICCMSE 2015, in Athens, Greece.
  • March 2015: The lab participares in the Workshop for Molecular Modeling and Drug Design, hosted by Scienomics.
  • February 2015: Evi and Zoe present talks in the 3rd NANODRUG meeting in Innsbruck, Austria.
  • January 2015: Katerina Zacharis is admitted to Cambridge University, UK to study Biology.
  • December 2014: Read our latest paper on Nanoparticle-Membrane interactions in PLOS Comput Biol.
  • November 2014: The Lab presents 8 posters and one invited talk at the "1st International Congress: From Drug Discovery to Drug Delivery" in Athens.
  • October 2014: Read our latest papers on understanding the overactivation mechanism of a PI3Kα mutant present in 30% of breast cancer patients in PLOS Comput Biol and on exploring PI3Kα allosterism in the J Phys Chem B.
  • October 2014: The lab participates in the HSCBB2014 Conference and Marilena Liosi wins the best poster award.
  • September 2014: Eva Lionta accepts a position to work in Pharmathen, R& D, Drug Delivery Division.
  • August 2014: Zoe attends the American Chemical Society Fall National Meeting in San Francisco and receives the OpenEye Outstanding Junior Faculty Award in Computational Chemistry. She also presents our work on PI3Ka and Arp2/3 in two talks.
  • August 2014: Marilena Liosi receives a travel grant award to attend the EMBL-EBI/Wellcome Workshop on Resources for Computational Drug Discovery 2014. 
  • June 2014: Harris Ioannidis is now a PhD student at the University of Cyprus and the EPOS-IASIS company with the FP7, ITN project: "Innovative, mechanistic-based strategies for delivery of therapeutic macromolecules across cellular and biological barriers".
  • May 2014: Zoe presents a talk on drug design in the 1st Athens Science Festival.
  • April 2014: Zoe presents our work on PI3Ka in the 2nd Hellenic Oncology Conference (Bioinformatics Workshop) in Thessaloniki.
  • April 2014: Zoe wins the OpenEye Outstanding Junior Faculty Award in Computational Chemistry from the American Chemical Society. 
  • April 2014: Evi, George, and Zoe present at the ICCMSE 2014 conference.
  • March 2014: Zoe attends the "New Approaches in Drug Design Workshop - The aspect of time in drug design, in Schloss Rauischholzhausen, Germany."
  • March 2014: George presents our latest work on designing new Arp2/3 inhibitors and on the losartan-bilayer-AT1 receptor interactions at the ACS Spring National Meeting in Dallas, USA.
  • February 2014: Zoe & George attend the "Advances and Progress in Drug Design Conference, in London, UK.
  • February 2014: Read how a typical day in the life of a computational chemist is!
  • January 2014: Read our latest paper on the molecular basis of action of the AT1 antagonist losartan.
  • January 2014: Eva leaves for 3 month practical training at Sanofi Aventis Frankfurt.
  • December 2013: Zoe Cournia and Hari Leontiadou present at the "PRACE Conference for Scientific Computing", Paphos, Cyprus.
  • November 2013: Zoe Cournia is invited to extend her service at the Editiorial Board Member of the AACR "Chemistry in Cancer Research" Group for 2014-2016.
  • November 2013: Zoe Cournia attends the Barcelona BioMed Conference "FRONTIERS IN DYNAMICS SIMULATIONS OF BIOLOGICAL MOLECULES" and presents our nanoparticle work.
  • October 2013: Hari Leontiadou wins the PRACE/LinkSCEEM fellowship for the Conference on Scientific Computing 2013 to be held in Cyprus 3-6 December 2013.
  • October 2013: The lab participates in the UberCloud HPC Experiment Round 3 with the project: "TEAM 61 – Using Cloud Computing to Perform Molecular Dynamics Simulations of the Mutant PI3Kα Protein". Download the full report here.
  • October 2013: Zoe Cournia attends the CECAM workshop: "Innovative Approaches to Computational Drug Discovery", October 1 to October 4, 2013, Lausanne, Switzerland and presents our work on "Protein flexibility in computer-aided drug design: The Arp2/3 and M2TM cases".
  • September 2013: Evi Gkeka wins the best poster presentation prize for her poster: "Studying the Influence of Cholesterol on Nanoparticle Partitioning into Lipid Membranes" at the CECAM workshop: Coupling between protein, water, and lipid dynamics in complex biological systems: Theory and Experiments.
  • September 2013: Zoe Cournia, Evi Gkeka, and George Patargias attend the CECAM workshop: Coupling between protein, water, and lipid dynamics in complex biological systems: Theory and Experiments and present our work on NP-membrane interactions and elucidating the molecular basis of losartan.
  • July 2013: Evi Gkeka presents our work on "Nanoparticle functionalization for optimal translocation across a lipid bilayer" in the Gordon Research Conference on Computer-Aided Drug Design in Mount Snow, VT, USA.
  • June 2013: Zoe Cournia presents our results on PI3Ka inhibition in the "Next-Gen Kinase Inhibitors" and "Structure-based drug design" conferences in Boston MA.
  • June 2013: The lab participates in the "Ubercloub experiment", where we will apply the cloud computing service model to workloads on remote Cluster Computing resources in the area of Computational Biology. 
  • April 2013: Zoe Cournia presents our work on Arp2/3 and nanoparticle-membrane interactions in the ACS Spring Meeting in New Orleans, USA.
  • April 2013: Zoe Cournia co-organizes the TEDMED Athens conference.
  • March 2013: Zoe Cournia, George Patargias, and collaborator Brad Nolen are awarded 11.2 Million core hours on the CURIE supercomputer in France for their proposal: "Arp2/3 - Mechanistic studies of the Arp2/3 complex activation", following a PRACE contest.
  • February 2013: Read our latest paper on Free Energy Calculations on ihibitors of the Influenza A/M2TM Pore.
  • February 2013: Evi Gkeka attends the Biophysical Society Meeting in Philadelphia, USA to present our work on PI3Ka simulations and Nanoparticle-Membrane interactions.
  • January 2013: Zoe Cournia  and Evi Gkeka are co-PIs in the SYNERGASIA II grant entitled: "Magnetic Nanoparticles for targeted MRI therapy".
  • January 2013: Zoe Cournia becomes an Editiorial Board Member of the AACR "Chemistry in Cancer Research" Group 2013-2014.
  • December 2012: Zoe Cournia is a co-organizer in the CECAM workshop: Coupling between protein, water, and lipid dynamics in complex biological systems: Theory and Experiments from September 24, 2013 to September 27, 2013, in CECAM-HQ-EPFL, Lausanne, Switzerland.
  • December 2012: Evi Gkeka receives the LinkSCEEM/Cy-Tera Travel grant to attend a GPU workshop at the Cyprus Institute.
  • November 2012: George Patargias, Zoe Cournia, and Brad Nolen receive access to HPC infrastructure provided by the HP-SEE project  and the LinkSCEEM/Cy-Tera project totalling 500,000 core hours for the Arp2/3 project.
  • November 2012: Evi Gkeka receives the CPOW Travel Award from the Biophysical Society attend the 57th National BPS Meeting in Philadelphia. She will be presenting two abstracts on our work in Nanoparticle-Membrane interactions and PI3Ka simulations.
  • September 2012: The lab participates in the 6th International Conference of The Hellenic Crystallographic Association with two talks on Arp2/3 inhibitors and PI3Kα MD simulations.
  • August 2012: Zoe presents a talk in the Molecular Modeling Conference in Queenstown, New Zealand entitled: "MD simulations of mutant and WT PI3Kα: Insights into the mechanism of oncogenesis and implications for drug design"
  • July 2012: Read Zoe's interview for the Heidelberg Alumni newsletter.
  • June 2012: Our publication on the optimization of a small-molecule inhibitor of the Arp2/3 complex is published in ChemMedChem and featured in the inside cover of the journal!
  • March 2012: Zoe Cournia attends the "New Approaches in Drug Design and Discovery" Workshop in Schloss Rauischholzhausen and the ACS National Meeting in San Diego and gives talks on our PI3Ka results.
  • November 2011: Eva Lionta wins the IKY National Fellowship for performing Master's studies in our group. She will work on the "Discovery of potent NURR1 activators using CADD for the treatment of Parkinson's Disease".
  • October 2011: Zoe Cournia wins the "Best Talk" Award at the "Innovative Approaches to to Computational Drug Discovery" CECAM Workshop in Lausanne, Switzerland.
  • October 2011: Evi Gkeka attends the "Coarse-Grained Biomolecular Modeling" CECAM Workshop in Lausanne, Switzerland.
  • September 2011: George Patargias is awarded a Postdoctoral Fellowship from the Greek General Secretariat for Research and Techology to work on "Mechanistic and Inhibition Studies of the Arp2/3 complex activation".
  • September 2011: Thomas Evangelidis receives a travel grant to attend the "Fast Methods for Long-Range Interactions in Complex Systems" CECAM - Jülich Summer School  at the Forschungszentrum Jülich, Germany.
  • March 2010: Thomas Evangelidis received a travel grant award to attend the DEISA/PRACE School entitled: “Tools and Techniques for Extreme Scalability”, held in Edinburgh, 29-31 March 2011. He is one of the three students selected from Greece to receive the award. 
  • Nov 2009: Zoe Cournia is a Co-PI at a Synergasia grant entitled: “PIK3CA Oncogenic Mutations in Breast and Colon Cancers: Development of Targeted Anticancer Drugs and Diagnostics”.
  • Oct 2009: Evi Gkeka attended the “Biomolecular interactions workshop” in Alexandroupoli, Greece.
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