Publications
2025
Scholarly publications
Chaillet, M., Roet, S., Veltkamp, R. C., & Förster, F. (2025). pytom-match-pick: A tophat-transform constraint for automated classification in template matching. Journal of Structural Biology: X, 11, 1-11. Article 100125. https://doi.org/10.1016/j.yjsbx.2025.100125
https://research-portal.uu.nl/ws/files/263537804/1-s2.0-S2590152425000066-main.pdf
https://research-portal.uu.nl/ws/files/263537804/1-s2.0-S2590152425000066-main.pdf
2024
Scholarly publications
Chaillet, M. L., Roet, S., Veltkamp, R. C., & Förster, F. (2024). pytom-match-pick: a tophat-transform constraint for automated classification in template matching. (pp. 1-25). bioRxiv. https://doi.org/10.1101/2024.09.17.613497
https://research-portal.uu.nl/ws/files/240485560/2024.09.17.613497v2.full.pdf
https://research-portal.uu.nl/ws/files/240485560/2024.09.17.613497v2.full.pdf
Vervust, W., Zhang, D. T., Ghysels, A., Roet, S., Erp, T. S. V., & Riccardi, E. (2024). PyRETIS 3: Conquering rare and slow events without boundaries. Journal of Computational Chemistry, 45(15), 1224-1234. https://doi.org/10.1002/jcc.27319
http://@https://dspace.library.uu.nl/bitstream/handle/1874/438474/J_Comput_Chem_-_2024_-_Vervust_-_PyRETIS_3_Conquering_rare_and_slow_events_without_boundaries.pdf?sequence=1
http://@https://dspace.library.uu.nl/bitstream/handle/1874/438474/J_Comput_Chem_-_2024_-_Vervust_-_PyRETIS_3_Conquering_rare_and_slow_events_without_boundaries.pdf?sequence=1
Zhang, D. T., Baldauf, L., Roet, S., Lervik, A., & van Erp, T. S. (2024). Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps. Proceedings of the National Academy of Sciences of the United States of America, 121(7), Article e2318731121. https://doi.org/10.1073/pnas.2318731121
http://@https://dspace.library.uu.nl/bitstream/handle/1874/437156/zhang-et-al-2024-highly-parallelizable-path-sampling-with-minimal-rejections-using-asynchronous-replica-exchange-and.pdf?sequence=1
http://@https://dspace.library.uu.nl/bitstream/handle/1874/437156/zhang-et-al-2024-highly-parallelizable-path-sampling-with-minimal-rejections-using-asynchronous-replica-exchange-and.pdf?sequence=1
2023
Scholarly publications
Chaillet, M. L., Schot, G. V. D., Gubins, I., Roet, S., Veltkamp, R. C., & Förster, F. (2023). Extensive Angular Sampling Enables the Sensitive Localization of Macromolecules in Electron Tomograms. International Journal of Molecular Sciences, 24(17), Article 13375. https://doi.org/10.3390/ijms241713375
http://@https://dspace.library.uu.nl/bitstream/handle/1874/434283/ijms-24-13375.pdf?sequence=1
http://@https://dspace.library.uu.nl/bitstream/handle/1874/434283/ijms-24-13375.pdf?sequence=1
2022
Scholarly publications
Mons, E., Roet, S., Kim, R. Q., & Mulder, M. P. C. (2022). A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations. Current Protocols, 2(6), Article e419. https://doi.org/10.1002/cpz1.419
Roet, S., Zhang, D. T., & van Erp, T. S. (2022). Exchanging Replicas with Unequal Cost, Infinitely and Permanently. Journal of Physical Chemistry A, 126(47), 8878-8886. https://doi.org/10.1021/acs.jpca.2c06004
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
2021
Scholarly publications
Ghysels, A., Roet, S., Davoudi, S., & Erp, T. S. V. (2021). Exact non-Markovian permeability from rare event simulations. Physical Review Research, 3(3), Article 033068. https://doi.org/10.1103/PhysRevResearch.3.033068
Roet, S., Daub, C. D., & Riccardi, E. (2021). Chemistrees: Data-Driven Identification of Reaction Pathways via Machine Learning. Journal of Chemical Theory and Computation, 17(10), 6193-6202. https://doi.org/10.1021/acs.jctc.1c00458
2020
Scholarly publications
Roet, S., Hooft, F., Bolhuis, P. G., Swenson, D. W. H., & Vreede, J. (2020, Feb 28). Path sampling simulations reveal how the Q61L mutation restricts the dynamics of KRas. bioRxiv. https://doi.org/10.1101/2020.02.28.969451
2019
Scholarly publications
Riccardi, E., Lervik, A., Roet, S. J. S., Aarøen, O., & van Erp, T. S. (2019). PyRETIS 2: An improbability drive for rare events. Journal of Computational Chemistry, 41(4), 370-377. https://doi.org/10.1002/jcc.26112