Dr. ir. I.M. (Ioana) Ilie
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Van 't Hoff Institute for Molecular Sciences
Bezoekadres
- Science Park 904
Postadres
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Postbus 94157
1090 GD Amsterdam
Contactgegevens
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Publicaties
2024
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]
2023
- 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]
2022
- 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]
2021
- 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
2019
- 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., Briels, W. J., & den Otter, W. K. (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., den Otter, W. K., & Briels, W. J. (2014). Rotational Brownian Dynamics of Clathrin Cage Formation. Journal of Chemical Physics, 141, 065101. https://doi.org/10.1063/1.4891306
Prijs / subsidie
- Ilie, I., Reek, J. & Fitzsimons, C. (2024). MMD hub grant: Digital development of drug nanocarriers for Alzheimer’s disease. https://hims.uva.nl/shared/faculteiten/en/faculteit-der-natuurwetenschappen-wiskunde-en-informatica/news/2024/07/nine-research-projects-chos…
- Ilie, I. (2022). Career Development Award.
Lidmaatschap / relevante positie
- Ilie, I. (2023). president, Assistant Professor Network. https://hims.uva.nl/content/news/2023/10/ioana-ilie-elected-president-of-assistant-professor-network-netherlands.html?origin=4zNaIwCsT1iMc%2FL4U9Sh2Q
- Ilie, I. (2022-). Assistant Professor Network.
Mediaoptreden
- Ilie, I. (05-08-2024). Podium: Ioana Ilie C2W. Podium: Ioana Ilie. https://www.sciencelink.net/features/podium-ioana-ilie/22117.article
Tijdschriftredactie
- Ilie, I. (editor) (2022). eLife (Journal).
- 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, ...).
This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list. -
Nevenwerkzaamheden
Geen nevenwerkzaamheden
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.