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ORCIDZoe Cournia
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2020 – today
- 2024
[j30]Raphaelle Versini, Sujith Sritharan, Burcu Aykaç Fas
, Thibault Tubiana, Sana Zineb Aimeur, Julien Henri, Marie Erard, Oliver Nüsse, Jessica Andreani, Marc Baaden, Patrick Fuchs, Tatiana Galochkina, Alexios Chatzigoulas, Zoe Cournia, Hubert Santuz, Sophie Sacquin-Mora, Antoine Taly:
A Perspective on the Prospective Use of AI in Protein Structure Prediction. J. Chem. Inf. Model. 64(1): 26-41 (2024)- [j29]Zoe Cournia, Christophe Chipot:
Applications of Free-Energy Calculations to Biomolecular Processes. A Collection. J. Chem. Inf. Model. 64(7): 2129-2131 (2024) - [j28]Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu:
Editorial: Machine Learning in Materials Science. J. Chem. Inf. Model. 64(10): 3959-3960 (2024) - [j27]Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos:
Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators. J. Chem. Inf. Model. 64(13): 5140-5150 (2024) - 2023
- [j26]Thereza A. Soares, Zoe Cournia, Kevin J. Naidoo, Rommie E. Amaro, Habibah A. Wahab, Kenneth M. Merz Jr.:
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. J. Chem. Inf. Model. 63(11): 3227-3229 (2023) - 2022
- [j25]Alexios Chatzigoulas, Zoe Cournia:
Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning. Briefings Bioinform. 23(2) (2022) - [j24]Alexios Chatzigoulas, Zoe Cournia:
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design. Bioinform. 38(24): 5449-5451 (2022) - [j23]Samanta Makurat, Zoe Cournia, Janusz Rak:
Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations. J. Chem. Inf. Model. 62(1): 142-149 (2022) - [j22]Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro:
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. J. Chem. Inf. Model. 62(24): 6287-6291 (2022) - 2021
- [j21]Stamatia Zavitsanou, Alexandros Tsengenes, Michail Papadourakis, Giorgio Amendola, Alexios Chatzigoulas, Dimitris Dellis, Sandro Cosconati, Zoe Cournia:
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations. J. Chem. Inf. Model. 61(9): 4131-4138 (2021) - [j20]Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro:
Advancing Women in Chemistry. J. Chem. Inf. Model. 61(11): 5305-5306 (2021) - 2020
- [j19]Evangelos Karatzas, Juan Eiros Zamora, Emmanouil Athanasiadis, Dimitris Dellis, Zoe Cournia, George M. Spyrou:
ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing. Bioinform. 36(8): 2602-2604 (2020) - [j18]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:
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. J. Comput. Aided Mol. Des. 34(5): 601-633 (2020) - [j17]Kira A. Armacost, Sereina Riniker, Zoe Cournia:
Novel Directions in Free Energy Methods and Applications. J. Chem. Inf. Model. 60(1): 1-5 (2020) - [j16]Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz Jr.:
Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. J. Chem. Inf. Model. 60(7): 3328-3330 (2020) - [j15]Zoe Cournia, Bryce K. Allen, Thijs Beuming, David A. Pearlman, Brian K. Radak, Woody Sherman:
Rigorous Free Energy Simulations in Virtual Screening. J. Chem. Inf. Model. 60(9): 4153-4169 (2020) - [j14]Kira A. Armacost, Sereina Riniker, Zoe Cournia:
Exploring Novel Directions in Free Energy Calculations. J. Chem. Inf. Model. 60(11): 5283-5286 (2020) - [j13]Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang:
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. 60(12): 5868-5869 (2020)
2010 – 2019
- 2019
- [j12]Alexios Chatzigoulas, Konstantina Karathanou, Dimitris Dellis, Zoe Cournia:
Correction to "NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit". J. Chem. Inf. Model. 59(4): 1681 (2019) - [j11]Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia:
A Celebration of Women in Computational Chemistry. J. Chem. Inf. Model. 59(5): 1683-1692 (2019) - 2018
- [j10]Christina Athanasiou, Sofia Vasilakaki, Dimitris Dellis, Zoe Cournia:
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. J. Comput. Aided Mol. Des. 32(1): 21-44 (2018) - [j9]Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia:
Women in Computational Chemistry. J. Chem. Inf. Model. 58(11): 2175-2177 (2018) - [j8]Alexios Chatzigoulas, Konstantina Karathanou, Dimitris Dellis, Zoe Cournia:
NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit. J. Chem. Inf. Model. 58(12): 2380-2386 (2018) - 2017
- [j7]Zoe Cournia, Bryce K. Allen, Woody Sherman:
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. J. Chem. Inf. Model. 57(12): 2911-2937 (2017) - 2016
- [j6]Harris Ioannidis, Antonios Drakopoulos, Christina Tzitzoglaki, Nadine Homeyer, Felix Kolarov, Paraskevi Gkeka, Kathrin Freudenberger, Christos Liolios, Günter Gauglitz, Zoe Cournia, Holger Gohlke, Antonios Kolocouris:
Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. J. Chem. Inf. Model. 56(5): 862-876 (2016) - 2014
- [j5]Paraskevi Gkeka, Thomas Evangelidis, Maria Pavlaki, Vasiliki Lazani, Savvas Christoforidis, Bogos Agianian, Zoe Cournia:
Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant. PLoS Comput. Biol. 10(10) (2014) - [j4]Paraskevi Gkeka, Panagiotis Angelikopoulos, Lev Sarkisov, Zoe Cournia:
Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion. PLoS Comput. Biol. 10(12) (2014) - 2012
- [j3]Emmanouil Athanasiadis, Zoe Cournia, George M. Spyrou:
ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery. Bioinform. 28(22): 3002-3003 (2012) - [c1]Paraskevi Gkeka, Emmanouil Athanasiadis, George M. Spyrou, Zoe Cournia:
Enhancing the effectiveness of virtual screening by using the ChemBioServer: Application to the discovery of PI3Kα inhibitors. BIBE 2012: 266-269
2000 – 2009
- 2005
- [j2]Andrea C. Vaiana, Zoe Cournia, Ion Bogdan Costescu, Jeremy C. Smith:
AFMM: A molecular mechanics force field vibrational parametrization program. Comput. Phys. Commun. 167(1): 34-42 (2005) - [j1]Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann:
A molecular mechanics force field for biologically important sterols. J. Comput. Chem. 26(13): 1383-1399 (2005)
Coauthor Index
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