Publications - Affiliation: Biomedical Research Foundation, Academy Of Athens
2024
[26] Free energy landscape of the PI3Kα C-terminal activation (, , and ), In Computational and Structural Biotechnology Journal, volume 23, . [bibtex] [url] [doi]
[25] Computational Investigation of BMAA and Its Carbamate Adducts as Potential GluR2 Modulators (, , , and ), In Journal of Chemical Information and Modeling, volume 64, . [bibtex] [url] [doi]
[24] Disentangling the riddle of systemic lupus erythematosus with antiphospholipid syndrome: blood transcriptome analysis reveals a less-pronounced IFN-signature and distinct molecular profiles in venous versus arterial events (, , , , , , , , , , , , and ), In Annals of the Rheumatic Diseases, BMJ Publishing Group Ltd, . [bibtex] [url] [doi]
2023
[23] Transcriptomic and proteomic profiling reveals distinct pathogenic features of peripheral non-classical monocytes in systemic lupus erythematosus (, , , , , , and ), In Clinical Immunology, volume 255, . [bibtex] [url] [doi]
[22] Martini 3 Force Field Parameters for Protein Lipidation Post-Translational Modifications (, , , , , , and ), In Journal of Chemical Theory and Computation, volume 19, . [bibtex] [url] [doi]
2022
[21] Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations (), In Journal of Chemical Information and Modeling, volume 62, . [bibtex] [url] [doi]
[20] Investigating the Bioactive Conformation of Angiotensin II Using Markov State Modeling Revisited with Web-Scale Clustering (), In Journal of Chemical Theory and Computation, volume 18, . [bibtex] [url] [doi]
[19] Membrane Composition and Raf[CRD]-Membrane Attachment Are Driving Forces for K-Ras4B Dimer Stability (), In The Journal of Physical Chemistry B, volume 126, . [bibtex] [url] [doi]
[18] Predicting protein–membrane interfaces of peripheral membrane proteins using ensemble machine learning (), In Briefings in Bioinformatics, . [bibtex] [url] [doi]
[17] DREAMM: a web-based server for drugging protein-membrane interfaces as a novel workflow for targeted drug design ( and ), In Bioinformatics, volume 38, . [bibtex] [url] [doi]
[16] Cross-species transcriptome analysis for early detection and specific therapeutic targeting of human lupus nephritis (), In Annals of the Rheumatic Diseases, volume 81, . [bibtex] [url] [doi]
[15] Combined – whole blood and skin fibroblasts- transcriptomic analysis in Psoriatic Arthritis reveals molecular signatures of activity, resistance and early response to treatment (), In Frontiers in Immunology, volume 13, . [bibtex] [url] [doi]
[14] Comparative Interaction Studies of Quercetin with 2-Hydroxyl-propyl-β-cyclodextrin and 2,6-Methylated-β-cyclodextrin (), In Molecules, volume 27, . [bibtex] [url] [doi]
2021
[13] FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations (), In J. Chem. Inf. Model., volume 61, . [bibtex] [url] [doi]
[12] Evaluating the Efficiency of the Martini Force Field to Study Protein Dimerization in Aqueous and Membrane Environments (), In J. Chem. Theory Comput., volume 17, . [bibtex] [url] [doi]
[11] The effect of S427F mutation on RXRα activity depends on its dimeric partner (), In Chem. Sci., . [bibtex] [url] [doi]
2020
[10] ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compoundsfacilitating both drug discovery and repurposing (), In Bioinformatics, volume , . [bibtex] [pdf] [doi]
[9] The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations (), In Journal of Computer-Aided Molecular Design, volume , . [bibtex] [url] [doi]
[8] Coating of magnetic nanoparticles affects their interactions with model cell membranes (), In Biochimica et Biophysica Acta (BBA) - General Subjects, volume 1864, . [bibtex] [url] [doi]
[7] Allostery in membrane proteins (), In Current Opinion in Structural Biology, volume 62, . [bibtex] [url] [doi]
[6] Unravelling the effect of the E545K mutation on PI3Kα kinase ( and ), In Chemical Science, volume , . [bibtex] [url] [doi]
[5] Transcriptome reprogramming and myeloid skewing in haematopoietic stem and progenitor cells in systemic lupus erythematosus (), In Annals of the Rheumatic Diseases, volume 79, . [bibtex] [url] [doi]
2018
[4] Insights into the mechanism of the PIK3CA E545K activating mutation using MD simulations. (, , and ), In Sci Rep, volume 8, . [bibtex] [url] [doi]
2017
[3] Magnetic nanoparticles coated with polyarabic acid demonstrate enhanced drug delivery and imaging properties for cancer theranostic applications (), In Scientific Reports, volume 7, . [bibtex] [url] [doi]
[2] Informed walks: whispering hints to gene hunters inside networks’ jungle (), In BMC systems biology, volume 11, . [bibtex] [url] [doi]
[1] 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 (), In Journal of Computer-Aided Molecular Design, . [bibtex] [url] [doi]