AFMM: A molecular mechanics force field vibrational parametrization program. - Andrea C. Vaiana; Zoe Cournia; Ion Bogdan Costescu; Jeremy C. Smith (Comput. Phys. Commun., 2005)

A molecular mechanics force field for biologically important sterols. - Zoe Cournia; Jeremy C. Smith; G. Matthias Ullmann (J. Comput. Chem., 2005)

Enhancing the effectiveness of virtual screening by using the ChemBioServer: Application to the discovery of PI3Kα inhibitors. - Paraskevi Gkeka; Emmanouil Athanasiadis; George M. Spyrou; Zoe Cournia (BIBE, 2012)

ChemBioServer: a web-based pipeline for filtering, clustering and visualization of chemical compounds used in drug discovery. - Emmanouil Athanasiadis; Zoe Cournia; George M. Spyrou (Bioinform., 2012)

Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion. - Paraskevi Gkeka; Panagiotis Angelikopoulos; Lev Sarkisov; Zoe Cournia (PLoS Comput. Biol., 2014)

Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant. - Paraskevi Gkeka; Thomas Evangelidis; Maria Pavlaki; Vasiliki Lazani; Savvas Christoforidis; Bogos Agianian; Zoe Cournia (PLoS Comput. Biol., 2014)

Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM. - Harris Ioannidis; Antonios Drakopoulos; Christina Tzitzoglaki; Nadine Homeyer; Felix Kolarov; Paraskevi Gkeka; Kathrin Freudenberger; Christos Liolios; Günter Gauglitz; Zoe Cournia; Holger Gohlke; Antonios Kolocouris (J. Chem. Inf. Model., 2016)

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. - Zoe Cournia; Bryce K. Allen; Woody Sherman (J. Chem. Inf. Model., 2017)

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. - Christina Athanasiou; Sofia Vasilakaki; Dimitris Dellis; Zoe Cournia (J. Comput. Aided Mol. Des., 2018)

NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit. - Alexios Chatzigoulas; Konstantina Karathanou; Dimitris Dellis; Zoe Cournia (J. Chem. Inf. Model., 2018)

Women in Computational Chemistry. - Habibah A. Wahab; Rommie E. Amaro; Zoe Cournia (J. Chem. Inf. Model., 2018)

Correction to "NanoCrystal: A Web-Based Crystallographic Tool for the Construction of Nanoparticles Based on Their Crystal Habit". - Alexios Chatzigoulas; Konstantina Karathanou; Dimitris Dellis; Zoe Cournia (J. Chem. Inf. Model., 2019)

A Celebration of Women in Computational Chemistry. - Habibah A. Wahab; Rommie E. Amaro; Zoe Cournia (J. Chem. Inf. Model., 2019)

ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing. - Evangelos Karatzas; Juan Eiros Zamora; Emmanouil Athanasiadis; Dimitris Dellis; Zoe Cournia; George M. Spyrou (Bioinform., 2020)

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; et al. (J. Comput. Aided Mol. Des., 2020)

Novel Directions in Free Energy Methods and Applications. - Kira A. Armacost; Sereina Riniker; Zoe Cournia (J. Chem. Inf. Model., 2020)

Exploring Novel Directions in Free Energy Calculations. - Kira A. Armacost; Sereina Riniker; Zoe Cournia (J. Chem. Inf. Model., 2020)

Rigorous Free Energy Simulations in Virtual Screening. - Zoe Cournia; Bryce K. Allen; Thijs Beuming; David A. Pearlman; Brian K. Radak; Woody Sherman (J. Chem. Inf. Model., 2020)

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. - Angelica Mazzolari; Ariane Nunes-Alves; Habibah A. Wahab; Rommie E. Amaro; Zoe Cournia; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2020)

Editorial: Method and Data Sharing and Reproducibility of Scientific Results. - Kenneth M. Merz Jr.; Rommie E. Amaro; Zoe Cournia; Matthias Rarey; Thereza A. Soares; Alexander Tropsha; Habibah A. Wahab; Renxiao Wang (J. Chem. Inf. Model., 2020)

Advancing Women in Chemistry. - Zoe Cournia; Thereza A. Soares; Habibah A. Wahab; Rommie E. Amaro (J. Chem. Inf. Model., 2021)

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 (J. Chem. Inf. Model., 2021)

Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning. - Alexios Chatzigoulas; Zoe Cournia (Briefings Bioinform., 2022)

Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. - Zoe Cournia; Thereza A. Soares; Habibah A. Wahab; Rommie E. Amaro (J. Chem. Inf. Model., 2022)

Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations. - Samanta Makurat; Zoe Cournia; Janusz Rak (J. Chem. Inf. Model., 2022)

DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design. - Alexios Chatzigoulas; Zoe Cournia (Bioinform., 2022)

Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. - Thereza A. Soares; Zoe Cournia; Kevin J. Naidoo; Rommie E. Amaro; Habibah A. Wahab; Kenneth M. Merz Jr. (J. Chem. Inf. Model., 2023)

Applications of Free-Energy Calculations to Biomolecular Processes. A Collection. - Zoe Cournia; Christophe Chipot (J. Chem. Inf. Model., 2024)

Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators. - Isidora Diakogiannaki; Michail Papadourakis; Vasileia Spyridaki; Zoe Cournia; Andreas Koutselos (J. Chem. Inf. Model., 2024)

Editorial: Machine Learning in Materials Science. - Kenneth M. Merz Jr.; Yee-Siew Choong; Zoe Cournia; Olexandr Isayev; Thereza A. Soares; Guo-Wei Wei 001; Feng Zhu 004 (J. Chem. Inf. Model., 2024)

A Perspective on the Prospective Use of AI in Protein Structure Prediction. - 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; et al. (J. Chem. Inf. Model., 2024)

Predicting RNA Structure Utilizing Attention from Pretrained Language Models. - Ioannis Papazoglou; Alexios Chatzigoulas; George Tsekenis; Zoe Cournia (J. Chem. Inf. Model., 2025)