Paraskevi Gkeka
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Allostery in its many disguises: from theory to applications
SJ Wodak, E Paci, NV Dokholyan, IN Berezovsky, A Horovitz, J Li, ...
Structure 27 (4), 566-578, 2019
Membrane protein structure, function, and dynamics: a perspective from experiments and theory
Z Cournia, TW Allen, I Andricioaei, B Antonny, D Baum, G Brannigan, ...
The Journal of membrane biology 248, 611-640, 2015
Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems
P Gkeka, G Stoltz, A Barati Farimani, Z Belkacemi, M Ceriotti, JD Chodera, ...
Journal of chemical theory and computation 16 (8), 4757-4775, 2020
DPPC-cholesterol phase diagram using coarse-grained Molecular Dynamics simulations
Y Wang, P Gkeka, JE Fuchs, KR Liedl, Z Cournia
Biochimica et Biophysica Acta (BBA)-Biomembranes 1858 (11), 2846-2857, 2016
Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations.
JPP Ramalho, P Gkeka, L Sarkisov
Langmuir 27 (7), 3723-3730, 2011
Investigating the Structure and Dynamics of the PIK3CA Wild-Type and H1047R Oncogenic Mutant
P Gkeka, T Evangelidis, M Pavlaki, V Lazani, S Christoforidis, B Agianian, ...
PLoS computational biology 10 (10), e1003895, 2014
Homogeneous hydrophobic–hydrophilic surface patterns enhance permeation of nanoparticles through lipid membranes
P Gkeka, L Sarkisov, P Angelikopoulos
The journal of physical chemistry letters 4 (11), 1907-1912, 2013
Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion
P Gkeka, P Angelikopoulos, L Sarkisov, Z Cournia
PLoS Comput Biol 10(12), e1003917, 2014
Interactions of phospholipid bilayers with several classes of amphiphilic α-helical peptides: insights from coarse-grained molecular dynamics simulations
P Gkeka, L Sarkisov
The journal of physical chemistry B 114 (2), 826-839, 2010
Self-assembly of anionic, ligand-coated nanoparticles in lipid membranes
P Angelikopoulos, L Sarkisov, Z Cournia, P Gkeka
Nanoscale, 1040-1048, 2016
Chasing collective variables using autoencoders and biased trajectories
Z Belkacemi, P Gkeka, T Lelièvre, G Stoltz
Journal of chemical theory and computation 18 (1), 59-78, 2021
Free energy calculations reveal the origin of binding preference for aminoadamantane blockers of influenza A/M2TM pore
P Gkeka, S Eleftheratos, A Kolocouris, Z Cournia
Journal of Chemical Theory and Computation 9 (2), 1272-1281, 2013
Exploring a non-ATP pocket for potential allosteric modulation of PI3Kα
P Gkeka, A Papafotika, S Christoforidis, Z Cournia
The Journal of Physical Chemistry B 119 (3), 1002-1016, 2015
Alchemical Free Energy Calculations and Isothermal Titration Calorimetry Measurements of Aminoadamantanes Bound to the Closed State of Influenza A/M2TM
H Ioannidis, A Drakopoulos, C Tzitzoglaki, N Homeyer, F Kolarov, ...
J. Chem. Inf. Model., 2016
Spontaneous formation of a barrel-stave pore in a coarse-grained model of the synthetic LS3 peptide and a DPPC lipid bilayer
P Gkeka, L Sarkisov
The Journal of Physical Chemistry B 113 (1), 6-8, 2009
Automated design of macrocycles for therapeutic applications: from small molecules to peptides and proteins
D Sindhikara, M Wagner, P Gkeka, S Güssregen, G Tiwari, G Hessler, ...
Journal of Medicinal Chemistry 63 (20), 12100-12115, 2020
Exercise training attenuates the development of cardiac autonomic dysfunction in diabetic rats
I Nakos, NPE Kadoglou, P Gkeka, AT Tzallas, N Giannakeas, ...
in vivo 32 (6), 1433-1441, 2018
Phase diagram of a stratum corneum lipid mixture
M Podewitz, Y Wang, P Gkeka, S von Grafenstein, KR Liedl, Z Cournia
The Journal of Physical Chemistry B 122 (46), 10505-10521, 2018
The role of patterned hydrophilic domains in nanoparticle-membrane interactions
P Gkeka, P Angelikopoulos
Current Nanoscience 7 (5), 690-698, 2011
Contact map fingerprints of protein-ligand unbinding trajectories reveal mechanisms determining residence times computed from Scaled Molecular Dynamics
M Bianciotto, P Gkeka, DB Kokh, R Wade, M Hervé, 2021
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