Publications

Wilson, C.J.; Karttunen, M.; de Groot, B. L.; Gapsys, V.: Accurately Predicting Protein pK_a Values Using Nonequilibrium Alchemy. Journal of Chemical Theory and Computation 19 (21), pp. 7833 - 7845 (2023)

Eltzner, B.; Hansen, P. E. H.; Huckemann, S. F.; Sommer, S.: Diffusion means in geometric spaces. Bernoulli 29 (4), pp. 3141 - 3170 (2023)

Wiechers, H.; Kehl, A.; Hiller, M.; Eltzner, B.; Huckemann, S.F.; Meyer, A.; Tkach, I.; Bennati, M.; Pokern, Y.: Bayesian optimization to estimate hyperfine couplings from ¹⁹F ENDOR spectra. Journal of Magnetic Resonance 353, 107491 (2023)

Kopec, W.; Thomson, A. S.; de Groot, B. L.; Rothberg, B. S.: Interactions between selectivity filter and pore helix control filter gating in the MthK channel. Journal of General Physiology 155 (8), e202213166 (2023)

Boothroyd, S.; Behara, P. K.; Madin, O. C.; Hahn, D. F.; Jang, H.; Gapsys, V.; Wagner, J. R.; Horton, J. T.; Dotson, D. L.; Thompson, M. W. et al.; Maat, J.; Gokey, T.; Wang, L.-P.; Cole, D. J.; Gilson, M. K.; Chodera, J. D.; Bayly, C. I.; Shirts, M. R.; Mobley, D. L.: Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation 19 (11), pp. 3251 - 3275 (2023)

Lam, C. K.; de Groot, B. L.: Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. Journal of Chemical Theory and Computation 19 (9), pp. 2574 - 2589 (2023)

Moore, J. H.; Margreitter, C.; Janet, J. P.; Engkvist, O.; de Groot, B. L.; Gapsys, V.: Automated relative binding free energy calculations from SMILES to ΔΔG. Communications Chemistry 6, 82 (2023)

Gu, R.-X.; de Groot, B. L.: Central cavity dehydration as a gating mechanism of potassium channels. Nature Communications 14 (1), 2178 (2023)

Matthes, D.; de Groot, B. L.: Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. The Journal of Biological Chemistry 299 (4), 103034 (2023)

Wiechers, H.; Eltzner, B.; Mardia, K. V.; Huckemann, S. F.: Learning torus PCA-based classification for multiscale RNA correction with application to SARS-CoV-2. Journal of the Royal Statistical Society - Series C: Applied Statistics 72 (2), pp. 271 - 293 (2023)

Hauke, L.; Primeßnig, A.; Eltzner, B.; Radwitz, J.; Huckemann, S. F.; Rehfeldt, F.: FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking. PLoS One 18 (2), e0279336 (2023)

Wieczor, M.; Genna, V.; Aranda, J.; Badia, R. M.; Lluis Gelpi, J.; Gapsys, V.; de Groot, B. L.; Lindahl, E.; Municoy, M.; Hospital, A. et al.; Orozco, M.: Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews: Computational Molecular Science 13 (1), e1622 (2023)