Dr I.M. (Ioana) Ilie
Faculty of Science
Van 't Hoff Institute for Molecular Sciences
Visiting address
- Science Park 904
Postal address
-
Postbus 94157
1090 GD Amsterdam
Contact details
-
Publications
2024
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
- Ilie, I. M. (2022). Antibody binding increases the flexibility of the prion protein. Biochimica et Biophysica Acta. Proteins and Proteomics, 1870, 140827.
- Ilie, I. M. (2022). Antibody binding modulates the dynamics of the membrane-bound prion protein. Biophysical Journal, 121, 1.
- Ilie, I. M. (2022). Interactions of Curcumin’s Degradation Products with the Aβ42 Dimer: A Computational Study. Journal of Physical Chemistry B, 126, 76267.
- 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). The role of the first transmembrane helix in bacterial YidC: Insights from the crystal structure and molecular dynamics simulations, Biochimica et Biophysica Acta Biomembranes, 1864, 183825. https://doi.org/10.1101/2021.07.15.452481
- Ilie, I. M. (2022). Thermostable designed ankyrin repeat proteins (DARPins) as building blocks for innovative drugs. The Journal of Biological Chemistry, 1, 101403.
2021
- Ilie, I. M. (2021). Flanking sequence preference modulated de novo DNA methylation in the mouse genome. Nucleic Acids Research, 49, 145-157.
2019
- Ilie, I. M. (2019). Simulation Studies of Amyloidogenic Peptides and their Aggregates. Chemical Reviews, 119, 6956-6993.
2018
- Ilie, I. M. (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.
- 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.
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. (2016). A coarse grained protein model with internal degrees of freedom. Application to α-synuclein aggregation. Journal of Chemical Physics, 144, 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
Prize / grant
- Ilie, I. (2022). Career Development Award.
Membership / relevant position
- 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.
Journal editor
- Ilie, I. (editor) (2022). eLife (Journal).
- Ilie, I. (editor) (2022). Frontiers: New approaches to Biophysical Investigation of Protein Disorder and Folding (Journal).
Talk / presentation
- 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.
Others
- 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, ...).
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Ancillary activities
No ancillary activities
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.