Publications of Berend L. de Groot

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)

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)

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)

Frieg, B.; Antonschmidt, L.; Dienemann, C.; Geraets, J. A.; Najbauer, E. E.; Matthes, D.; de Groot, B. L.; Andreas, L. B.; Becker, S.; Griesinger, C. et al.; Schröder, G. F.: The 3D structure of lipidic fibrils of α-synuclein. Nature Communications 13 (1), 6810 (2022)

Khalak, Y.; Tresadern, G.; Hahn, D. F.; de Groot, B. L.; Gapsys, V.: Chemical Space Exploration with Active Learning and Alchemical Free Energies. Journal of Chemical Theory and Computation 18 (10), pp. 6259 - 6270 (2022)

Antonschmidt, L.; Matthes, D.; Dervişoğlu, R.; Frieg, B.; Dienemann, C.; Leonov, A.; Nimerovsky, E.; Sant, V.; Ryazanov, S.; Giese, A. et al.; Schröder, G.; Becker, S.; de Groot, B. L.; Griesinger, C.; Andreas, L. B.: The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nature Communications 13, pp. 5385 - 5394 (2022)

Kutzner, C.; Kniep, C.; Cherian, A.; Nordstrom, L.; Grubmüller, H.; de Groot, B. L.; Gapsys, V.: GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. Journal of Chemical Infomation and Modeling 62 (7), pp. 1691 - 1711 (2022)

Gapsys, V.; Hahn, D. F.; Tresadern, G.; Mobley, D. L.; Rampp, M.; de Groot, B.: Pre-exascale computing of protein-ligand binding free energies with open source software for drug design. Journal of Chemical Information and Modeling 62 (5), pp. 1172 - 1177 (2022)

Öster, C.; Tekwani Movellan, K.; Goold, B.; Hendriks, K.; Lange, S.; Becker, S.; de Groot, B. L.; Kopec, W.; Andreas, L. B.; Lange, A.: Direct detection of bound ammonium ions in the selectivity filter of ion channels by solid-state NMR. Journal of the American Chemical Society 144 (9), pp. 4147 - 4157 (2022)

Kim, M.; Ha, J.-H.; Choi, J.; Kim, B.-R.; Gapsys, V.; Lee, K. O.; Jee, J.-G.; Chakrabarti, K. S.; de Groot, B. L.; Griesinger, C. et al.; Ryu, K.-S.; Lee, D.: Repositioning food and drug administration-approved drugs for inhibiting Biliverdin IXβ reductase B as a novel thrombocytopenia therapeutic target. Journal of Medicinal Chemistry 65 (3), pp. 2548 - 2557 (2022)

Chakrabarti, K. S.; Olsson, S.; Pratihar, S.; Giller, K.; Overkamp, K.; Lee, K. O.; Gapsys, V.; Ryu, K.-S.; de Groot, B. L.; Noé, F. et al.; Becker, S.; Lee, D.; Weikl, T. R.; Griesinger, C.: A litmus test for classifying recognition mechanisms of transiently binding proteins. Nature Communications 13, 3792 (2022)

Khalak, Y.; Tresadern, G.; Aldeghi, M.; Baumann, H.; Mobley, D.; de Groot, B. L.; Gapsys, V.: Alchemical absolute protein-ligand binding free energies for drug design. Chemical Science 12, pp. 13958 - 13971 (2021)

Mironenko, A.; Zachariae, U.; de Groot, B. L.; Kopec, W.: The persistent question of potassium channel permeation mechanisms. Journal of Molecular Biology 433 (17), 167002 (2021)

Gapsys, V.; Yildirim, A.; Aldeghi, M.; Khalak, Y.; van der Spoel, D.; de Groot, B. L.: Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 4, 61 (2021)

Roy, R. N.; Hendriks, K.; Kopec, W.; Abdolvand, S.; Weiss, K. L.; de Groot, B. L.; Lange, A.; Sun, H.; Coates, L.: Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ 8 (3), pp. 421 - 430 (2021)

Baumann, H. M.; Gapsys, V.; de Groot, B. L.; Mobley, D. L.: Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations. Journal of Physical Chemistry B 125 (17), pp. 4241 - 4261 (2021)

Werner, M.; Gapsys, V.; de Groot, B. L.: One plus one makes three: Triangular coupling of correlated amino acid mutations. Journal of Physical Chemistry Letters 12 (12), pp. 3195 - 3201 (2021)