Publications

2025

• T. Vlaar, B.M. Mayer, L.P. van der Heide & I.M. Ilie*, Computational design of Bax-inhibiting peptides, Mat. Adv. 6, 2160-2169 (2025) - Emerging Investigator Highlight & cover feature

• G. Giannetti, F. Matsumura, F. Caporaletti, D. Micha, G.H. Koenderink, I.M. Ilie, M. Bonn, S. Woutersen, G. Giubertoni, Water and Collagen: a Mystery yet to Unfold, Biomacromolec. In press (2025)

2024

• M. Paesani and I.M. Ilie*, Metaparticles: Computationally engineered nanomaterials with tunable and responsive properties, J. Chem. Phys., 161, 244905 (2024) – selected 2024 Editor’s choice & Emerging Investigator Special Collection, featured on the journal cover
• G. Giubertoni, S. Chagri, P.G. Argudo, L. Prädel, D. Maltseva, A. Greco, F. Caporaletti, A. Pavan, I.M. Ilie*, Y. Ren, D.Y.W. Ng, M. Bonn, T. Weil, S. Woutersen, Structural adaptability and surface activity of peptides derived from tardigrade proteins, Prot. Sci., 33, e5153 (2024)
• J. Zhou, S. Assenza, M. Tatli, J. Tian, I.M. Ilie, F.S. Ruggeri, E.L. Starostin, A. Caflisch, T.P.J. Knowles, G.Dietler, H. Stahlberg, S.K. Sekatskii and R Mezzenga, Hierarchical Protofilament Intertwining rules the Formation of Mixed-Curvature Amyloid Polymorphs, Adv. Sci., 2402740 (2024)
• C. Durukan, F. Arbore, R. Klintrot, C. Bigiotti, I.M. Ilie, J. Vreede, T.N. Grossmann, S. Hennig, Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF− Y, ChemBioChem 25 (9), e202400020 (2024)
• G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F.Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S.Woutersen, Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration, PNAS 121 (11), e2313162121 (2024)
• D. de Raffele and I.M. Ilie*, Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning, Chem. Commun.,  60, 632 – 645 (2024)

2023

1. G. Giubertoni et al. Structural adaptability and surface activity of tardigrade-inspired peptides, bioRxiv (2023)

2. I.M.Ilie*, C.Ehrhardt, A. Caflisch and G. Weitz-Schmidt, Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations, JCIM, 63, 3878 (2023) 

2022

1. M. Haji-Dehabadi, A. Caflisch, I.M. Ilie*, R. Firouzi, Interactions of Curcumin’s Degradation Products with the Aβ42 Dimer: A Computational Study, J. Phys. Chem. B. 126, 7627 (2022)

2. I.M.Ilie* and A. Caflisch, Antibody binding increases the flexibility of the prion protein, BBA - Proteins and Proteomics 1870, 140827 (2022)

3. I.M.Ilie, M. Bacci, A. Vitalis, A. Caflisch, Antibody binding modulates the dynamics of the membrane-bound prion protein, Biophys. J., 121, 1 (2022)

4. S. García-Viñuales, I.M.Ilie (co-first author), A.M. Santoro, V. Romanucci, A. Zarrelli, G. Di Fabio, A. Caflisch, D. Milardi, Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions, BBA - Proteins and Proteomics, 140772 (2022)

5. K. J. Nass, I.M. Ilie* (co-first author), M.J. Saller, A.J.M. Driessen, A. Caflisch, R.A. Kammerer, X. Li, The role of the first transmembrane helix in bacterial YidC: Insights from the crystal structure and molecular dynamics simulations, BBA - Biomembranes, 1864, 183825 (2022)

6. J. Schilling, C. Jost, I.M. Ilie, J. Schnabl, O. Buechi, R. Sakariah Eapen, R. Truffer, A. Caflisch, P. Forrer,Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs, J. Biol. Chem., 1, 101403 (2022)

2021

1. I. Mallona, I.M. Ilie, M. Manzo, A. Caflisch and T. Baubec, Flanking sequence preference modulated de novo DNA methylation in the mouse genome, Nucl. Acids Res., 49, 145-157 (2021)

2019

1. I.M. Ilie* and A. Caflisch, Simulation Studies of Amyloidogenic Peptides and their Aggregates. Chem. Rev., 119, 6956-6993 (2019)

2018

1. I.M. Ilie* and A. Caflisch, Disorder at the tips of a disease-relevant Aβ amyloid fibril. A Molecular Dynamics study. J. Phys. Chem. B, 122, 11072–11082 (2018) 

2. I.M. Ilie*, D. Nayar, W.K. den Otter, N. F. A. van der Vegt and W.J. Briels, Intrinsic conformational preferences in α-synuclein fibrils: Insights from Molecular Dynamics Simulations, J.C.T.C. 14, 3298–3310 (2018)

2017

1. I.M. Ilie*, W.K. den Otter and W.J. Briels, The attachment of α-synuclein to a fiber: a coarse-grain approach, J. Chem. Phys., 146, 115102 (2017)

2016

1. I.M. Ilie*, W.K. den Otter and W.J. Briels, A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation, J. Chem. Phys., 144, 085103 (2016)

2015

1. I.M. Ilie, W.J. Briels and W.K. den Otter, An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles, J. Chem. Phys., 142, 114103 (2015)

2014

1. I.M. Ilie, W.K. den Otter and W.J. Briels, Rotational Brownian Dynamics of Clathrin Cage Formation,  J.Chem. Phys., 141, 065101 (2014).