[20] | Cross-species transcriptome analysis for early detection and specific therapeutic targeting of human lupus nephritis (Frangou Eleni, Garantziotis Panagiotis, Grigoriou Maria, Banos Aggelos, Nikolopoulos Dionysis, Pieta Antigone, Doumas Stavros A, Fanouriakis Antonis, Hatzioannou Aikaterini, Manolakou Theodora, Alissafi Themis, Verginis Panayotis, Athanasiadis Emmanouil, Dermitzakis Emmanouil, Bertsias George, Filia Anastasia, Boumpas Dimitrios T), In Annals of the Rheumatic Diseases, volume 81, 2022. |
[19] | Combined – whole blood and skin fibroblasts- transcriptomic analysis in Psoriatic Arthritis reveals molecular signatures of activity, resistance and early response to treatment (Grivas Alexandros, Grigoriou Maria, Malissovas Nikos, Sentis George, Filia Anastasia, Flouda Sofia, Katsimpri Pelagia, Verginis Panayotis, Boumpas Dimitrios T.), In Frontiers in Immunology, volume 13, 2022. |
[18] | Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering (Christoforou Emmanouil, Leontiadou Hari, Noé Frank, Samios Jannis, Emiris Ioannis Z., Cournia Zoe), In Journal of Chemical Theory and Computation, volume 18, 2022. |
[17] | Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin (Vakali Vasiliki, Papadourakis Michail, Georgiou Nikitas, Zoupanou Nikoletta, Diamantis Dimitrios A., Javornik Uroš, Papakyriakopoulou Paraskevi, Plavec Janez, Valsami Georgia, Tzakos Andreas G., Tzeli Demeter, Cournia Zoe, Mauromoustakos Thomas), In Molecules, volume 27, 2022. |
[16] | Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning (Chatzigoulas Alexios, Cournia Zoe), In Briefings in Bioinformatics, 2022. |
[15] | Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations (Makurat Samanta, Cournia Zoe, Rak Janusz), In Journal of Chemical Information and Modeling, volume 62, 2022. |
[14] | Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability (Andreadelis Ioannis, Kiriakidi Sofia, Lamprakis Christos, Theodoropoulou Anastasia, Doerr Stefan, Chatzigoulas Alexios, Manchester John, Velez-Vega Camilo, Duca José S., Cournia Zoe), In The Journal of Physical Chemistry B, volume 126, 2022. |
[13] | The effect of S427F mutation on RXRα activity depends on its dimeric partner (Ioannis Galdadas, Vangelis Bonis, Paraskevi Vgenopoulou, Michail Papadourakis, Panos Kakoulidis, Georgia Stergiou, Zoe Cournia, Apostolos Klinakis), In Chem. Sci., 2021. |
[12] | FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations (Stamatia Zavitsanou, Alexandros Tsengenes, Michail Papadourakis, Giorgio Amendola, Alexios Chatzigoulas, Dimitris Dellis, Sandro Cosconati, Zoe Cournia), In J. Chem. Inf. Model., volume 61, 2021. |
[11] | Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments (Christos Lamprakis, Ioannis Andreadelis, John Manchester, Camilo Velez-Vega, José S. Duca, Zoe Cournia), In J. Chem. Theory Comput., volume 17, 2021. |
[10] | Transcriptome reprogramming and myeloid skewing in haematopoietic stem and progenitor cells in systemic lupus erythematosus (Grigoriou Maria, Banos Aggelos, Filia Anastasia, Pavlidis Pavlos, Giannouli Stavroula, Karali Vassiliki, Nikolopoulos Dionysis, Pieta Antigone, Bertsias George, Verginis Panayotis, Mitroulis,Ioannis, Boumpas Dimitrios T), In Annals of the Rheumatic Diseases, volume 79, 2020. |
[9] | Coating of magnetic nanoparticles affects their interactions with model cell membranes (Michalis Lazaratos, Konstantina Karathanou, Eleftherios Mainas, Alexios Chatzigoulas, Natassa Pippa, Costas Demetzos, Zoe Cournia), In Biochimica et Biophysica Acta (BBA) - General Subjects, volume 1864, 2020. |
[8] | Allostery in membrane proteins (Zoe Cournia, AlexiosChatzigoulas), In Current Opinion in Structural Biology, volume 62, 2020. |
[7] | Unravelling the effect of the E545K mutation on PI3Kα kinase (Ioannis Galdadas, Francesco Luigi Gervasio and Zoe Cournia), In Chemical Science, volume , 2020. |
[6] | The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations (Andrea Rizzi, Travis Jensen, David R. Slochower, Matteo Aldeghi, Vytautas Gapsys, Dimitris Ntekoumes, Stefano Bosisio, Michail Papadourakis, Niel M. Henriksen, Bert L. de Groot, Zoe Cournia, Alex Dickson, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera), In Journal of Computer-Aided Molecular Design, volume , 2020. |
[5] | ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compoundsfacilitating both drug discovery and repurposing (Evangelos Karatzas, Juan Eiros Zamora, Emmanouil Athanasiadis, Dimitris Dellis, Zoe Cournia, George M. Spyrou), In Bioinformatics, volume , 2020. |
[4] | Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations. (Leontiadou, H., Galdadas, I., Athanasiou, C. and Cournia, Z.), In Sci Rep, volume 8, 2018. |
[3] | Informed walks: whispering hints to gene hunters inside networks’ jungle (Bourdakou Marilena M, Spyrou George M), In BMC systems biology, volume 11, 2017. |
[2] | Magnetic nanoparticles coated with polyarabic acid demonstrate enhanced drug delivery and imaging properties for cancer theranostic applications (Patitsa, Maria and Karathanou, Konstantina and Kanaki, Zoi and Tzioga, Lamprini and Pippa, Natassa and Demetzos, Constantinos and Verganelakis, Dimitris A. and Cournia, Zoe and Klinakis, Apostolos), In Scientific Reports, volume 7, 2017. |
[1] | 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 and Vasilakaki, Sofia and Dellis, Dimitris and Cournia, Zoe), In Journal of Computer-Aided Molecular Design, 2017. |