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Results: 81
Number of items: 81
  • Open Access
    Chen, L. (2026). Molecular dynamics guided analysis of Bacillus subtilis spore germination mechanisms. [Thesis, fully internal, Universiteit van Amsterdam].
  • Open Access
    Zhuo, L. (2026). Molecular modelling of electrocatalytic CO2 conversion. [Thesis, fully internal, Universiteit van Amsterdam].
  • Open Access
    Abbondanzieri, E. A., Badrinarayanan, A. B., Barillà, D., Bell, S. D., Blombach, F., Bouet, J. Y., Bulgheresi, S., Cao, Q. A. D., Dame, R. T., Dekker, C., Demuysere, M., Espéli, O., Fogg, P. C. M., Freddolino, P. L., Ganji, M., Gerson, T. M., Grainger, D. C., Hamoen, L. W., Harju, J., ... Zhang, Z. (2025). Future Directions of the Prokaryotic Chromosome Field. Molecular Microbiology, 123(2), 89-100. https://doi.org/10.1111/mmi.15347
  • Open Access
    van Heesch, T. (2025). Molecular codes in motion: Simulations of specificity, stability, and structural adaptation in protein-DNA complexes. [Thesis, fully internal, Universiteit van Amsterdam].
  • Schwab, S., Deiss, S., van Heesch, T., Joiner, J. D., Vreede, J., Hartmann, M. D., Lupas, A. N., Alvarez, B. H., Hu, Y., Escudeiro, P., & Alva, V. (2024, April 10). Data underlying the publication: Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending [Data set]. 4TU.ResearchData. https://doi.org/10.4121/6c07e4bb-96f1-4ee0-88ef-6978bda27e5d.v2
  • Vreede, J., Ilie, I., Hennig, S., Grossmann, T. N., & Bigiotti, C. (2024, March 8). Stapled peptide in complex with transcription factor NF-Y [Data set]. Universiteit van Amsterdam. https://doi.org/10.21942/uva.25368475.v1
  • Mohr, B. J., Vreede, J., Pérez de Alba Ortíz, A., & van Heesch, T. (2024, March 21). WIRES - Enhanced sampling strategies for the molecular simulation of DNA [Data set]. Universiteit van Amsterdam. https://doi.org/10.21942/uva.24745611.v3
  • Open Access
    Mohr, B., van Heesch, T., Pérez de Alba Ortíz, A., & Vreede, J. (2024). Enhanced sampling strategies for molecular simulation of DNA. Wiley interdisciplinary reviews. Computational molecular science , 14(2), Article e1712. https://doi.org/10.1002/wcms.1712
  • Open Access
    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
  • Open Access
    van Heesch, T., van de Lagemaat, E. M., & Vreede, J. (2024). Deciphering Sequence-Specific DNA Binding by H-NS Using Molecular Simulation. In R. T. Dame (Ed.), Bacterial Chromatin: Methods and Protocols (2nd ed., pp. 585-609). (Methods in molecular biology; Vol. 2819). Humana Press. https://doi.org/10.1007/978-1-0716-3930-6_27
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