Zoe Cournia

According to our database, Zoe Cournia authored at least 29 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

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, Alexios Chatzigoulas, Zoe Cournia, Hubert Santuz, Sophie Sacquin-Mora, Antoine Taly

J. Chem. Inf. Model., January, 2024

Applications of Free-Energy Calculations to Biomolecular Processes. A Collection.

Zoe Cournia, Christophe Chipot

J. Chem. Inf. Model., 2024

2023

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., June, 2023

2022

DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design.

Alexios Chatzigoulas, Zoe Cournia

Bioinform., December, 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

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

Predicting protein-membrane interfaces of peripheral membrane proteins using ensemble machine learning.

Alexios Chatzigoulas, Zoe Cournia

Briefings Bioinform., 2022

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

Advancing Women in Chemistry.

Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro

J. Chem. Inf. Model., 2021

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

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

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

Exploring Novel Directions in Free Energy Calculations.

Kira A. Armacost, Sereina Riniker, Zoe Cournia

J. Chem. Inf. Model., 2020

Novel Directions in Free Energy Methods and Applications.

Kira A. Armacost, Sereina Riniker, Zoe Cournia

J. Chem. Inf. Model., 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, Julien Michel, Michael K. Gilson, Michael R. Shirts, David L. Mobley, John D. Chodera

J. Comput. Aided Mol. Des., 2020

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

2019

A Celebration of Women in Computational Chemistry.

Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia

J. Chem. Inf. Model., 2019

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

2018

Women in Computational Chemistry.

Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia

J. Chem. Inf. Model., 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

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

2017

Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.

Zoe Cournia, Bryce K. Allen, Woody Sherman

J. Chem. Inf. Model., December, 2017

2016

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

2014

Investigating the Structure and Dynamics of the <i>PIK3CA</i> Wild-Type and H1047R Oncogenic Mutant.

Paraskevi Gkeka, Thomas Evangelidis, Maria Pavlaki, Vasiliki Lazani, Savvas Christoforidis, Bogos Agianian, Zoe Cournia

PLoS Comput. Biol., 2014

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

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

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

Proceedings of the 12th IEEE International Conference on Bioinformatics & Bioengineering, 2012

2005

A molecular mechanics force field for biologically important sterols.

Zoe Cournia, Jeremy C. Smith, G. Matthias Ullmann

J. Comput. Chem., 2005

AFMM: A molecular mechanics force field vibrational parametrization program.

Andrea C. Vaiana, Zoe Cournia, Ion Bogdan Costescu, Jeremy C. Smith

Comput. Phys. Commun., 2005