Search results

  • Full text

  • Document type

    • Publication year

  • Organisation

Results: 11
Number of items: 11
  • Open Access
    Roet, S., Hooft, F., Bolhuis, P. G., Swenson, D. W. H., & Vreede, J. (2022). Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas. Journal of Physical Chemistry B, 126(48), 10034-10044. https://doi.org/10.1021/acs.jpcb.2c06235
  • Open Access
    Bolhuis, P. G., & Swenson, D. W. H. (2021). Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook. Advanced Theory and Simulations, 4(4), Article 2000237. https://doi.org/10.1002/adts.202000237
  • 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
    Swenson, D. W. H., Prinz, J.-H., Noe, F., Chodera, J. D., & Bolhuis, P. G. (2019). OpenPathSampling: A Python Framework for Path Sampling Simulations. 1: Basics. Journal of Chemical Theory and Computation, 15(2), 813-836. https://doi.org/10.1021/acs.jctc.8b00626
  • 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
    Swenson, D. W. H., Prinz, J.-H., Noe, F., Chodera, J. D., & Bolhuis, P. G. (2019). OpenPathSampling: A Python Framework for Path Sampling Simulations. 2: Building and Customizing Path Ensembles and Sample Schemes. Journal of Chemical Theory and Computation, 15(2), 837-856. https://doi.org/10.1021/acs.jctc.8b00627
  • Open Access
    The PLUMED consortium (2019). Promoting transparency and reproducibility in enhanced molecular simulations. Nature Methods, 16(8), 670-673. https://doi.org/10.1038/s41592-019-0506-8
  • 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
  • Open Access
    Newton, A. C., Kools, R., Swenson, D. W. H., & Bolhuis, P. G. (2017). The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids. Journal of Chemical Physics, 147(15), Article 155101. https://doi.org/10.1063/1.5006485
  • Open Access
    Vreede, J., Bolhuis, P. G., & Swenson, D. W. H. (2016). Predicting the Mechanism and Kinetics of the Watson-Crick to Hoogsteen Base Pairing Transition. Biophysical Journal, 110(3, suppl. 1), 563A-564A. https://doi.org/10.1016/j.bpj.2015.11.3014
Page 1 of 2