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)

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)

Chasing Collective Variables using Autoencoders and biased trajectories. - Zineb Belkacemi; Paraskevi Gkeka; Tony Lelièvre; Gabriel Stoltz (CoRR, 2021)

HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design. - Francesco P. Panei; Rachel Torchet; Hervé Ménager; Paraskevi Gkeka; Massimiliano Bonomi (Bioinform., 2022)