Search results
Results: 81
Number of items: 81
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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 -
van Heesch, T., Vreede, J., & Bolhuis, P. G. (2023). SMD Simulations of ETS Inverse Sequence [Data set]. Figshare. https://doi.org/10.6084/m9.figshare.24161295.v1
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van Heesch, T., Bolhuis, P. G., & Vreede, J. (2023). SMD Simulations of GC-analogue Sequence [Data set]. Figshare. https://doi.org/10.6084/m9.figshare.22182562.v1
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van Heesch, T., Vreede, J., & Bolhuis, P. G. (2023). SMD Simulations of High Affinity Sequence [Data set]. Figshare. https://doi.org/10.6084/m9.figshare.21304482.v1
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Bolhuis, P. G., Vreede, J., & van Heesch, T. (2023). SMD Simulations of ETS Consensus Sequence [Data set]. Figshare. https://doi.org/10.6084/m9.figshare.24161280.v1
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van Heesch, T., Vreede, J., & Bolhuis, P. G. (2023). SMD Simulations of ETS Anti Sequence [Data set]. Figshare. https://doi.org/10.6084/m9.figshare.24161301.v1
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Hu, Y., Schwab, S., Deiss, S., Escudeiro, P., van Heesch, T., D. Joiner, J., Vreede, J., Hartmann, M. D., Lupas, A. N., Alvarez, B. H., Alva, V., & Dame, R. T. (2023, November 27). Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10211306
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van Heesch, T., Bolhuis, P. G., & Vreede, J. (2023). Decoding dissociation of sequence-specific protein-DNA complexes with non-equilibrium simulations. Nucleic Acids Research, 51(22), 12150-12160. https://doi.org/10.1093/nar/gkad1014
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Voorspoels, A., Vreede, J., & Carlon, E. (2023). Rigid Base Biasing in Molecular Dynamics Enables Enhanced Sampling of DNA Conformations. Journal of Chemical Theory and Computation, 19(3), 902-909. https://doi.org/10.1021/acs.jctc.2c00889
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Vreede, J. (2022, August 14). EntF*-D10 [Data set]. Universiteit van Amsterdam. https://doi.org/10.21942/uva.20485338.v2
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