Durukan, C., Arbore, F., Klintrot, R., Bigiotti, C., Ilie, I. M., Vreede, J., Grossmann, T. N., & Hennig, S. (2024). Binding Dynamics of a Stapled Peptide Targeting the Transcription Factor NF−Y. ChemBioChem, 25(9), Article e202400020. https://doi.org/10.1002/cbic.202400020[details]
Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., van der Net, A., Castro-Linares, G., Caporaletti, F., Micha, D., Hunger, J., Deblais, A., Bonn, D., Sommerdijk, N., Šarić, A., Ilie, I. M., Koenderink, G. H., & Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America, 121(11), Article e2313162121. https://doi.org/10.1073/pnas.2313162121[details]
Zhou, J., Assenza, S., Tatli, M., Tian, J., Ilie, I. M., Starostin, E. L., Caflisch, A., Knowles, T. P. J., Dietler, G., Ruggeri, F. S., Stahlberg, H., Sekatskii, S. K., & Mezzenga, R. (2024). Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs. Advanced Science, 11(32), Article 2402740. https://doi.org/10.1002/advs.202402740[details]
de Raffele, D., & Ilie, I. M. (2024). Unlocking novel therapies: cyclic peptide design for amyloidogenic targets through synergies of experiments, simulations, and machine learning. Chemical Communications, 60(6), 632-645. https://doi.org/10.1039/d3cc04630c[details]
Ilie, I. M., Ehrhardt, C., Caflisch, A., & Weitz-Schmidt, G. (2023). Decrypting Integrins by Mixed-Solvent Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 63(12), 3878-3891. https://doi.org/10.1021/acs.jcim.3c00480[details]
Dehabadi, M. H., Caflisch, A., Ilie, I. M., & Firouzi, R. (2022). Interactions of Curcumin’s Degradation Products with the Aβ42 Dimer: A Computational Study. Journal of Physical Chemistry B, 126(39), Article 76267. https://doi.org/10.1021/acs.jpcb.2c05846[details]
Ilie, I. M. (2022). Silybins inhibit human IAPP amyloid growth and toxicity through stereospecific interactions. Biochimica et Biophysica Acta. Proteins and Proteomics, 1870.
Ilie, I. M. (2022). Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The Journal of Biological Chemistry, 1, 101403.
Ilie, I. M., & Caflisch, A. (2022). Antibody binding increases the flexibility of the prion protein. Biochimica et Biophysica Acta. Proteins and Proteomics, 1870(11-12), Article 140827. https://doi.org/10.1016/j.bbapap.2022.140827[details]
Ilie, I. M., Bacci, M., Vitalis, A., & Caflisch, A. (2022). Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophysical Journal, 121(14), 2813-2825. https://doi.org/10.1016/j.bpj.2022.06.007[details]
Nass, K. J., Ilie, I. M., Saller, M. J., Driessen, A. J. M., Caflisch, A., Kammerer, R. A., & Li, X. (2022). The role of the N-terminal amphipathic helix in bacterial YidC: Insights from functional studies, the crystal structure and molecular dynamics simulations. Biochimica et Biophysica Acta Biomembranes, 1864(3), Article 183825. https://doi.org/10.1016/j.bbamem.2021.183825[details]
Mallona, I., Ilie, I. M., Karemaker, I. D., Butz, S., Manzo, M., Caflisch, A., & Baubec, T. (2021). Flanking sequence preference modulated de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49, 145-157. https://doi.org/10.1093/nar/gkaa1168
Ilie, I. M., & Caflisch, A. (2019). Simulation Studies of Amyloidogenic Peptides and their Aggregates. Chemical Reviews, 119(12), 6956-6993. https://doi.org/10.1021/acs.chemrev.8b00731
2018
Ilie, I. M. (2018). Intrinsic conformational preferences in α-synuclein fibrils: Insights from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 14, 3298-3310.
Ilie, I. M., & Caflisch, A. (2018). Disorder at the tips of a disease-relevant Aβ amyloid fibril. A Molecular Dynamics study. The journal of Physical Chemistry. B, 122, 11072-11083. https://doi.org/10.1021/acs.jpcb.8b05236
2017
Ilie, I. M. (2017). The attachment of α-synuclein to a fiber: a coarse-grain approach. Journal of Chemical Physics, 146, 115102. https://doi.org/10.1063/1.4978297
2016
Ilie, I. M., den Otter, W. K., & Briels, W. (2016). A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation. Journal of Chemical Physics, 144(8), 085103. https://doi.org/10.1063/1.4942115
2015
Ilie, I. M. (2015). An elementary singularity-free Rotational Brownian Dynamics algorithm for anisotropic particles. Journal of Chemical Physics, 142, 114103. https://doi.org/10.1063/1.4914322
2014
Ilie, I. M. (2014). Rotational Brownian Dynamics of Clathrin Cage Formation. Journal of Chemical Physics, 141, 065101. https://doi.org/10.1063/1.4891306
Ilie, I. (editor) (2022). Frontiers: New approaches to Biophysical Investigation of Protein Disorder and Folding (Journal).
Spreker
Ilie, I. (speaker) (22-11-2022). Rationally designed peptides to inhibit prion toxicity, Synapsis Forum, Gerzensee.
Ilie, I. (speaker) (14-11-2022). Antibody binding modulates the dynamics of the cellular prion protein, Lennard Jones Seminars.
Ilie, I. (speaker) (14-11-2022). Multiscale simulations of biomolecular systems, Dutch Soft Matter Meeting, Wageningen.
Ilie, I. (speaker) (1-10-2022). Antibody binding modulates the dynamics of the membrane-bound prion protein, Dutch Biophysics.
Ilie, I. (speaker) (1-9-2022). Antibody binding modulates the dynamics of the cellular prion protein, IDP Seminars.
Ilie, I. (speaker) (12-5-2022). Multiscale simulations of protein folding, aggregation and disease inhibition, Molecular Bases of Proteinopathies Symposium.
Ilie, I. (speaker) (31-1-2022). Antibody binding modulates the dynamics of the cellular prion protein, II Physics Postgraduate Weel, Lavras.
Andere
Ilie, I. (organiser) (29-6-2023 - 30-6-2023). NextGenChem@NL (organising a conference, workshop, ...).
Ilie, I. (other) (1-1-2023). Outreach: Jury member Akademikus/AkademiX (other).
Ilie, I. (participant) (21-9-2022). CHAINS, Veldhoven (participating in a conference, workshop, ...).
Ilie, I. (participant) (1-9-2022). StatMech Erice (IT) (participating in a conference, workshop, ...).
Ilie, I. (participant) (1-5-2022). NWO Life (participating in a conference, workshop, ...).
Ilie, I. (participant) (1-4-2022). KNCV-CTC-PhD+ Seminars. KNCV-CTC-PhD+ Seminars supported by the Computational and Theoretical Chemistry (CTC) division of the Royal Netherlands Chemical Society (KNCV) (organising a conference, workshop, ...).
Ilie, I. (organiser) (2022). KNCV-CTC-PhD+ Seminar series (organising a conference, workshop, ...).
De UvA gebruikt cookies voor het meten, optimaliseren en goed laten functioneren van de website. Ook worden er cookies geplaatst om inhoud van derden te kunnen tonen en voor marketingdoeleinden. Klik op ‘Accepteren’ om akkoord te gaan met het plaatsen van alle cookies. Of kies voor ‘Weigeren’ om alleen functionele en analytische cookies te accepteren. Je kunt je voorkeur op ieder moment wijzigen door op de link ‘Cookie instellingen’ te klikken die je onderaan iedere pagina vindt. Lees ook het UvA Privacy statement.