Search results

  • Full text

  • Document type

    • Publication year

  • Organisation

Results: 81
Number of items: 81
  • Vreede, J., Roet, S., Swenson, D., Hooft, F., & Bolhuis, P. (2020, February 22). Multiple State Transition Path Sampling simulations of KRas, wild type and oncogenic mutant Q61L [Data set]. Universiteit van Amsterdam. https://doi.org/10.21942/uva.11865579.v1
  • Open Access
    Qin, L., Ben Bdira, F., Sterckx, Y. G. J., Volkov, A. N., Vreede, J., Giachin, G., van Schaik, P., Ubbink, M., & Dame, R. T. (2020). Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Research, 48(4), 2156-2172. https://doi.org/10.1093/nar/gkz1226
  • Vreede, J. (2019, October 3). Predicting the mechanism and rate of H-NS binding to AT-rich DNA [Data set]. Universiteit van Amsterdam. https://doi.org/10.21942/uva.6960098
  • Open Access
    Vreede, J., Pérez de Alba Ortíz, A., Bolhuis, P. G., & Swenson, D. W. H. (2019). Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA. Nucleic Acids Research, 47(21), 11069-11076. https://doi.org/10.1093/nar/gkz837
  • Open Access
    Pérez de Alba Ortíz, A., Vreede, J., & Ensing, B. (2019). The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions. In M. Bonomi, & C. Camilloni (Eds.), Biomolecular Simulations: Methods and Protocols (pp. 255–290). (Methods in Molecular Biology; Vol. 2022). Humana Press. https://doi.org/10.1007/978-1-4939-9608-7_11
  • Open Access
    Riccardi, E., van Mastbergen, E. C., Navarre, W. W., & Vreede, J. (2019). Predicting the mechanism and rate of H-NS binding to AT-rich DNA. PLoS Computational Biology, 15(3), Article e1006845. https://doi.org/10.1371/journal.pcbi.1006845
  • Open Access
    Dubbeldam, D., Vreede, J., Vlugt, T. J. H., & Calero, S. (2019). Highlights of (bio-)chemical tools and visualization software for computational science. Current Opinion in Chemical Engineering, 23, 1-13. https://doi.org/10.1016/j.coche.2019.02.001
  • Open Access
    Wodak, S. J., Paci, E., Dokholyan, N. V., Berezovsky, I. N., Horovitz, A., Li, J., Hilser, V. J., Bahar, I., Karanicolas, J., Stock, G., Hamm, P., Stote, R. H., Eberhardt, J., Chebaro, Y., Dejaegere, A., Cecchini, M., Changeux, J.-P., Bolhuis, P. G., Vreede, J., ... McLeish, T. (2019). Allostery in Its Many Disguises: From Theory to Applications. Structure, 27(4), 566-578. https://doi.org/10.1016/j.str.2019.01.003
  • Open Access
    Muždalo, A., Saalfrank, P., Vreede, J., & Santer, M. (2018). Cis-to-Trans Isomerization of Azobenzene Derivatives Studied with Transition Path Sampling and Quantum Mechanical/Molecular Mechanical Molecular Dynamics. Journal of Chemical Theory and Computation, 14(4), 2042-2051. https://doi.org/10.1021/acs.jctc.7b01120
  • Open Access
    Vreede, J., Bolhuis, P. G., & Swenson, D. W. H. (2017). Path Sampling Simulations of the Mechanisms and Rates of Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA. Biophysical Journal, 112(3, Supplement 1), 214a. https://doi.org/10.1016/j.bpj.2016.11.1181
Page 5 of 9