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| [17] | 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. |
| [16] | 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. |
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| [15] | Biodegradation of Cellulose in Laboratory-Scale Bioreactors: Experimental and Numerical Studies (Mistriotis, Antonis, Papardaki, Nikoleta-Georgia and Provata, Astero), In Journal of Polymers and the Environment, 2019. |
| [14] | Shear Rheology of Unentangled and Marginally Entangled Ring Polymer Melts from Large-Scale Nonequilibrium Molecular Dynamics Simulations (Tsamopoulos, Alexandros J., Katsarou, Anna F., Tsalikis, Dimitrios G. and Mavrantzas, Vlasis G.), In Polymers, volume 11, 2019. |
| [13] | Structural characterization and molecular dynamics simulations of the caprine and bovine solute carrier family 11 A1 (SLC11A1) (Triantaphyllopoulos, Kostas A.and Baltoumas, Fotis A. and Hamodrakas, Stavros J.), In Journal of Computer-Aided Molecular Design, volume 33, 2019. |
| [12] | The gram-negative outer membrane modeler: Automated building of lipopolysaccharide-rich bacterial outer membranes in four force fields (Baltoumas, Fotis A., Hamodrakas, Stavros J. and Iconomidou, Vassiliki A.), In Journal of Computational Chemistry, volume 40, 2019. |
| [11] | Delving into the amyloidogenic core of human leukocyte chemotactic factor 2 (Paraskevi L. Tsiolaki, Georgia I. Nasi, Fotis A. Baltoumas, Shannon Fishman, Ho-Chou Tu and Vassiliki A. Iconomidou), In Journal of Structural Biology, 2019. |
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| [10] | 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. |
| [9] | Discovery of Novel Adenosine Receptor Antagonists through a Combined Structure- and Ligand-Based Approach Followed by Molecular Dynamics Investigation of Ligand Binding Mode (Lagarias, Panagiotis, Vrontaki, Eleni, Lambrinidis, George, Stamatis, Dimitrios, Convertino, Marino, Ortore, Gabriella, Mavromoustakos, Thomas, Klotz, Karl-Norbert and Kolocouris, Antonios), In Journal of Chemical Information and Modeling, volume 58, 2018. |
| [8] | αCGRP, another amyloidogenic member of the CGRP family (Paraskevi L. Tsiolaki, Georgia I. Nasi, Fotis A. Baltoumas, Nikolaos N. Louros, Vassiliki Magafa, Stavros J. Hamodrakas and Vassiliki A. Iconomidou), In Journal of Structural Biology, volume 203, 2018. |
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| [7] | 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. |
| [6] | 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. |
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| [5] | Fractal and multifractal analysis of PET/CT images of metastatic melanoma before and after treatment with ipilimumab (Breki, Christina-Marina and Dimitrakopoulou-Strauss, Antonia and Hassel, Jessica and Theoharis, Theoharis and Sachpekidis, Christos and Pan, Leyun and Provata, Astero), In EJNMMI Research, volume 6, 2016. |
| [4] | DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts (Paraskevopoulou, Maria D., Vlachos, Ioannis S., Karagkouni, Dimitra, Georgakilas, Georgios, Kanellos, Ilias, Vergoulis, Thanasis, Zagganas, Konstantinos, Tsanakas, Panayiotis, Floros, Evangelos, Dalamagas, Theodore and Hatzigeorgiou, Artemis G.), In Nucleic Acids Research, volume 44, 2016. |
| [3] | DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators (Georgakilas, Georgios, Vlachos, Ioannis S., Zagganas, Konstantinos, Vergoulis, Thanasis, Paraskevopoulou, Maria D., Kanellos, Ilias, Tsanakas, Panayiotis, Dellis, Dimitris, Fevgas, Athanasios, Dalamagas, Theodore and Hatzigeorgiou, Artemis G.), In Nucleic Acids Research, volume 44, 2016. |
| [2] | Molecular dynamics simulations and structure-based network analysis reveal structural and functional aspects of G-protein coupled receptor dimer interactions (Baltoumas, Fotis A. and Theodoropoulou, Margarita C. and Hamodrakas, Stavros J.), In Journal of Computer-Aided Molecular Design, volume 30, 2016. |
| [1] | A $\beta$-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils (Louros, Nikolaos N. and Baltoumas, Fotis A. and Hamodrakas, Stavros J. and Iconomidou, Vassiliki A.), In Journal of Computer-Aided Molecular Design, volume 30, 2016. |
