Publications

2.

Journal Article

Wilson, C. J.; Gapsys, V.; de Groot, B. L.: Improving pK_a Predictions with Reparameterized Force Fields and Free Energy Calculations. Journal of Chemical Theory and Computation 21 (8), pp. 4095 - 4106 (2025)

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3.

Journal Article

Amaro, R. E.; Åqvist, J.; Bahar, I.; Battistini, F.; Bellaiche, A.; Beltran, D.; Biggin, P. C.; Bonomi, M.; Bowman, G. R.; Bryce, R. A. et al.; Bussi, G.; Carloni, P.; Case, D. A.; Cavalli, A.; Chang, C.-E. A.; Cheatham, T. E.; Cheung, M. S.; Chipot, C.; Chong, L. T.; Choudhary, P.; Cisneros, G. A.; Clementi, C.; Collepardo-Guevara, R.; Coveney, P.; Covino, R.; Crawford, T. D.; Dal Peraro, M.; de Groot, B. L.; Delemotte, L.; De Vivo, M.; Essex, J. W.; Fraternali, F.; Gao, J.; Gelpí, J. L.; Gervasio, F. L.; González-Nilo, F. D.; Grubmüller, H.; Guenza, M. G.; Guzman, H. V.; Harris, S.; Head-Gordon, T.; Hernandez, R.; Hospital, A.; Huang, N.; Huang, X.; Hummer, G.; Iglesias-Fernández, J.; Jensen, J. H.; Jha, S.; Jiao, W.; Jorgensen, W. L.; Kamerlin, S. C. L.; Khalid, S.; Laughton, C.; Levitt, M.; Limongelli, V.; Lindahl, E.; Lindorff-Larsen, K.; Loverde, S.; Lundborg, M.; Luo, Y. L.; Luque, F. J.; Lynch, C. I.; MacKerell, A. D.; Magistrato, A.; Marrink, S. J.; Martin, H.; McCammon, J. A.; Merz, K.; Moliner, V.; Mulholland, A. J.; Murad, S.; Naganathan, A. N.; Nangia, S.; Noe, F.; Noy, A.; Oláh, J.; O’Mara, M. L.; Ondrechen, M. J.; Onuchic, J. N.; Onufriev, A.; Osuna, S.; Palermo, G.; Panchenko, A. R.; Pantano, S.; Parish, C.; Parrinello, M.; Perez, A.; Perez-Acle, T.; Perilla, J. R.; Pettitt, B. M.; Pietropaolo, A.; Piquemal, J.-P.; Poma, A. B.; Praprotnik, M.; Ramos, M. J.; Ren, P.; Reuter, N.; Roitberg, A.; Rosta, E.; Rovira, C.; Roux, B.; Rothlisberger, U.; Sanbonmatsu, K. Y.; Schlick, T.; Shaytan, A. K.; Simmerling, C.; Smith, J. C.; Sugita, Y.; Świderek, K.; Taiji, M.; Tao, P.; Tieleman, D. P.; Tikhonova, I. G.; Tirado-Rives, J.; Tuñón, I.; van der Kamp, M. W.; van der Spoel, D.; Velankar, S.; Voth, G. A.; Wade, R.; Warshel, A.; Welborn, V. V.; Wetmore, S. D.; Wheeler, T. J.; Wong, C. F.; Yang, L.-W.; Zacharias, M.; Orozco, M.: The need to implement FAIR principles in biomolecular simulations. Nature Methods 22, pp. 641 - 645 (2025)

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4.

Journal Article

Singh, S.; Gapsys, V.; Aldeghi, M.; Schaller, D.; Rangwala, A. M.; White, J. B.; Bluck, J. P.; Scheen, J.; Glass, W. G.; Guo, J. et al.; Hayat, S.; de Groot, B. L.; Volkamer, A.; Christ, C. D.; Seeliger, M. A.; Chodera, J. D.: Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding. The Journal of Physical Chemistry B 129 (11), pp. 2882 - 2902 (2025)

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5.

Journal Article

Kutzner, C.; Miletić, V.; Palacio Rodríguez, K.; Rampp, M.; Hummer, G.; de Groot, B. L.; Grubmüller, H.: Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. Journal of Computational Chemistry 46 (5), e70059 (2025)

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6.

Journal Article

Hehlert, P.; Effertz, T.; Gu, R.-X.; Nadrowski, B.; Geurten, B. R. H.; Beutner, D.; de Groot, B. L.; Göpfert, M. C.: NOMPC ion channel hinge forms a gating spring that initiates mechanosensation. Nature Neuroscience 28, pp. 259 - 267 (2025)

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7.

Journal Article

Sant, V.; Matthes, D.; Mazal, H.; Antonschmidt, L.; Wieser, F.; Movellan, K. T.; Xue, K.; Nimerovsky, E.; Stampolaki, M.; Nathan, M. et al.; Riedel, D.; Becker, S.; Sandoghdar, V.; de Groot, B. L.; Griesinger, C.; Andreas, L. B.: Lipidic folding pathway of α-Synuclein via a toxic oligomer. Nature Communications 16, 760 (2025)

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8.

Journal Article

Gapsys, V.; Kopec, W.; Matthes, D.; de Groot, B. L.: Biomolecular simulations at the exascale: From drug design to organelles and beyond. Current Opinion in Structural Biology 88, 102887 (2024)

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9.

Journal Article

Mendez-Otalvaro, E.; Kopec, W.; de Groot, B. L.: Effect of two activators on the gating of a K_2P channel. Biophysical Journal 123 (19), pp. 3408 - 3420 (2024)

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10.

Journal Article

Chiu, P.-L.; Orjuela, J. D.; de Groot, B. L.; Aponte Santamaría, C.; Walz, T.: Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 12, RP90851 (2024)

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11.

Journal Article

Mironenko, A.; de Groot, B. L.; Kopec, W.: Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS Nexus 3 (7), pgae272 (2024)

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12.

Journal Article

Wilson, C. J.; de Groot, B. L.; Gapsys, V.: Resolving coupled pH titrations using alchemical free energy calculations. Journal of Computational Chemistry 45 (17), pp. 1444 - 1455 (2024)

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13.

Journal Article

Hahn, D. F.; Gapsys, V.; de Groot, B. L.; Mobley, D. L.; Tresadern, G.: Current State of Open Source Force Fields in Protein–Ligand Binding Affinity Predictions. Journal of Chemical Information and Modeling 64 (13), pp. 5063 - 5076 (2024)

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pre-print

14.

Journal Article

Huang, P.; Abacka, H.; Wilson, C. J.; Wind, M. L.; Rutzler, M.; Hagstroem-Andersson, A.; Gourdon, P.; de Groot, B. L.; Venskutonyte, R.; Lindkvist-Petersson, K.: Molecular basis for human aquaporin inhibition. PNAS 121 (7), e2319682121 (2024)

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15.

Journal Article

Petrov, D.; Perthold, J.W.; Oostenbrink, C.; de Groot, B. L.; Gapsys, V.: Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of Chemical Theory and Computation 20 (2), pp. 914 - 925 (2024)

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16.

Journal Article

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)

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17.

Journal Article

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)

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18.

Journal Article

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)

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19.

Journal Article

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)

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20.

Journal Article

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)

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21.

Journal Article

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

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22.

Journal Article

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

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23.

Journal Article

Wieczór, 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)

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24.

Journal Article

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)

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25.

Journal Article

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)

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26.

Journal Article

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, 5385 (2022)

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27.

Journal Article

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 Information and Modeling 62 (7), pp. 1691 - 1711 (2022)

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pre-print

28.

Journal Article

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)

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29.

Journal Article

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)

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30.

Journal Article

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)

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31.

Journal Article

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)

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32.

Journal Article

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)

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33.

Journal Article

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)

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34.

Journal Article

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)

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35.

Journal Article

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)

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36.

Journal Article

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)

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37.

Journal Article

Buelens, F. P.; Leonov, H.; de Groot, B. L.; Grubmüller, H.: ATP-magnesium coordination: Protein structure-based force field evaluation and corrections. Journal of Chemical Theory and Computation 17 (3), pp. 1922 - 1930 (2021)

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38.

Journal Article

Daday, C.; de Groot, B. L.: Lipid–protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal 50 (2), pp. 181 - 186 (2021)

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39.

Journal Article

de Groot, B. L.; Janshoff, A.; Steinem, C.; Zweckstetter, M.: Special issue: Multicomponent lipid membranes—how molecular organisation leads to function. European Biophysics Journal 50 (2), pp. 107 - 108 (2021)

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40.

Journal Article

Najbauer, E.; Becker, S.; Giller, K.; Zweckstetter, M.; Lange, A.; Steinem, C.; de Groot, B. L.; Griesinger, C.; Andreas, L. B.: Structure, gating and interactions of the voltage-dependent anion channel. European Biophysics Journal 50 (2), pp. 159 - 172 (2021)

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41.

Journal Article

Zhang, Y.; Daday, C.; Gu, R. X.; Cox, C. D.; Martinac, B.; de Groot, B. L.; Walz, T.: Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 590 (7846), pp. 509 - 514 (2021)

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42.

Journal Article

Khalak, Y.; Tresadern, G.; de Groot, B. L.; Gapsys, V.: Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of Computer-Aided Molecular Design 35 (1), pp. 49 - 61 (2021)

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43.

Journal Article

Rabe von Pappenheim, F.; Aldeghi, M.; Shome, B.; Begley, T.; de Groot, B. L.; Tittmann, K.: Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine. Nature Chemical Biology 16 (11), p. 1237-1245 (2020)

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ZIP

44.

Journal Article

Gapsys, V.; de Groot, B. L.: On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 9, e57589 (2020)

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45.

Journal Article

Langan, P. S.; Vandavasi, V. G.; Kopec, W.; Sullivan, B.; Afonne, P. V.; Weiss, K. L.; de Groot, B. L.; Coates, L.: The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ 7 (5), pp. 835 - 843 (2020)

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46.

Journal Article

Schubeis, T.; Le Marchand, T.; Daday, C.; Kopec, W.; Tekwani Movellan, K.; Stanek, J.; Schwarzer, T. S.; Castiglione, K.; de Groot, B. L.; Pintacuda, G. et al.; Andreas, L. B.: A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences of the United States of America 117 (35), pp. 21014 - 21021 (2020)

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47.

Journal Article

Bastys, T.; Gapsys, V.; Walter, H.; Heger, E.; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.; Kalinina, O. V.: Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 17, 13 (2020)

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48.

Journal Article

Gu, R. X.; de Groot, B. L.: Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nature Communications 11, 2162 (2020)

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49.

Journal Article

Rizzi, A.; Jensen, T.; Slochower, D. R.; Aldeghi, M.; Gapsys, V.; Ntekoumes, D.; Bosisio, S.; Papadourakis, M.; Henriksen, N. M.; de Groot, B. L. et al.; Cournia, Z.; Dickson, A.; Michel, J.; Gilson, M. K.; Shirts, M. R.; Mobley, D. L.; Chodera, J. D.: The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design 34 (5), pp. 601 - 633 (2020)

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pre-print

50.

Journal Article

Gapsys, V.; Khabiri, M.; de Groot, B. L.; Freddolino, P. L.: Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes". The Journal of Physical Chemistry B 124 (6), pp. 1115 - 1123 (2020)

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