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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]
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
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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