Zoe Cournia

32 papers C 1Journal 31
YearRankTypeTitle / Venue / Authors
2025 J jnl
Predicting RNA Structure Utilizing Attention from Pretrained Language Models.
J. Chem. Inf. Model.
Ioannis Papazoglou, Alexios Chatzigoulas, George Tsekenis, Zoe Cournia
2024 J jnl
A Perspective on the Prospective Use of AI in Protein Structure Prediction.
J. Chem. Inf. Model.
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
2024 J jnl
Applications of Free-Energy Calculations to Biomolecular Processes. A Collection.
J. Chem. Inf. Model.
Zoe Cournia, Christophe Chipot
2024 J jnl
Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators.
J. Chem. Inf. Model.
Isidora Diakogiannaki, Michail Papadourakis, Vasileia Spyridaki, Zoe Cournia, Andreas Koutselos
2024 J jnl
Editorial: Machine Learning in Materials Science.
J. Chem. Inf. Model.
Kenneth M. Merz Jr., Yee-Siew Choong, Zoe Cournia, Olexandr Isayev, Thereza A. Soares, Guo-Wei Wei, Feng Zhu
2023 J jnl
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications.
J. Chem. Inf. Model.
Thereza A. Soares, Zoe Cournia, Kevin J. Naidoo, Rommie E. Amaro, Habibah A. Wahab, Kenneth M. Merz Jr.
2022 J jnl
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry.
J. Chem. Inf. Model.
Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro
2022 J jnl
DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design.
Bioinform.
Alexios Chatzigoulas, Zoe Cournia
2022 J jnl
Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations.
J. Chem. Inf. Model.
Samanta Makurat, Zoe Cournia, Janusz Rak
2022 J jnl
Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning.
Briefings Bioinform.
Alexios Chatzigoulas, Zoe Cournia
2021 J jnl
Advancing Women in Chemistry.
J. Chem. Inf. Model.
Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro
2021 J jnl
FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations.
J. Chem. Inf. Model.
Stamatia Zavitsanou, Alexandros Tsengenes, Michail Papadourakis, Giorgio Amendola, Alexios Chatzigoulas, Dimitris Dellis, Sandro Cosconati, Zoe Cournia
2020 J jnl
ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing.
Bioinform.
Evangelos Karatzas, Juan Eiros Zamora, Emmanouil Athanasiadis, Dimitris Dellis, Zoe Cournia, George M. Spyrou
2020 J jnl
Editorial: Method and Data Sharing and Reproducibility of Scientific Results.
J. Chem. Inf. Model.
Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
2020 J jnl
Exploring Novel Directions in Free Energy Calculations.
J. Chem. Inf. Model.
Kira A. Armacost, Sereina Riniker, Zoe Cournia
2020 J jnl
Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry.
J. Chem. Inf. Model.
Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz Jr.
2020 J jnl
Novel Directions in Free Energy Methods and Applications.
J. Chem. Inf. Model.
Kira A. Armacost, Sereina Riniker, Zoe Cournia
2020 J jnl
Rigorous Free Energy Simulations in Virtual Screening.
J. Chem. Inf. Model.
Zoe Cournia, Bryce K. Allen, Thijs Beuming, David A. Pearlman, Brian K. Radak, Woody Sherman
2020 J jnl
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.
J. Comput. Aided Mol. Des.
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
2019 J jnl
A Celebration of Women in Computational Chemistry.
J. Chem. Inf. Model.
Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia
2019 J jnl
Correction to "NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit".
J. Chem. Inf. Model.
Alexios Chatzigoulas, Konstantina Karathanou, Dimitris Dellis, Zoe Cournia
2018 J jnl
NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit.
J. Chem. Inf. Model.
Alexios Chatzigoulas, Konstantina Karathanou, Dimitris Dellis, Zoe Cournia
2018 J jnl
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.
Christina Athanasiou, Sofia Vasilakaki, Dimitris Dellis, Zoe Cournia
2018 J jnl
Women in Computational Chemistry.
J. Chem. Inf. Model.
Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia
2017 J jnl
Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.
J. Chem. Inf. Model.
Zoe Cournia, Bryce K. Allen, Woody Sherman
2016 J jnl
Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM.
J. Chem. Inf. Model.
Harris Ioannidis, Antonios Drakopoulos, Christina Tzitzoglaki, Nadine Homeyer, Felix Kolarov, Paraskevi Gkeka, Kathrin Freudenberger, Christos Liolios, Günter Gauglitz, Zoe Cournia, Holger Gohlke, Antonios Kolocouris
2014 J jnl
Investigating the Structure and Dynamics of the
PLoS Comput. Biol.
Paraskevi Gkeka, Thomas Evangelidis, Maria Pavlaki, Vasiliki Lazani, Savvas Christoforidis, Bogos Agianian, Zoe Cournia
2014 J jnl
Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion.
PLoS Comput. Biol.
Paraskevi Gkeka, Panagiotis Angelikopoulos, Lev Sarkisov, Zoe Cournia
2012 J jnl
ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery.
Bioinform.
Emmanouil Athanasiadis, Zoe Cournia, George M. Spyrou
2012 C conf
Enhancing the effectiveness of virtual screening by using the ChemBioServer: Application to the discovery of PI3Kα inhibitors.
BIBE
Paraskevi Gkeka, Emmanouil Athanasiadis, George M. Spyrou, Zoe Cournia
2005 J jnl
A molecular mechanics force field for biologically important sterols.
J. Comput. Chem.
Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann
2005 J jnl
AFMM: A molecular mechanics force field vibrational parametrization program.
Comput. Phys. Commun.
Andrea C. Vaiana, Zoe Cournia, Ion Bogdan Costescu, Jeremy C. Smith