Publikationen

2.

Zeitschriftenartikel

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), S. 3408 - 3420 (2024)

MPG.PuRe

3.

Zeitschriftenartikel

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

MPG.PuRe

4.

Zeitschriftenartikel

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

MPG.PuRe

5.

Zeitschriftenartikel

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), S. 5063 - 5076 (2024)

MPG.PuRe

6.

Zeitschriftenartikel

Vanegas, L. J.; Eltzner, B.; Rudolf, D.; Dura, M.; Lehnart, S. E.; Munk, A.: Analyzing cross-talk between superimposed signals: Vector norm dependent hidden Markov models and applications to ion channels. The Annals of Applied Statistics 18 (2), S. 1445 - 1470 (2024)

MPG.PuRe

7.

Zeitschriftenartikel

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)

MPG.PuRe

8.

Zeitschriftenartikel

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), S. 914 - 925 (2024)

MPG.PuRe

9.

Zeitschriftenartikel

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), S. 7833 - 7845 (2023)

MPG.PuRe

10.

Zeitschriftenartikel

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)

MPG.PuRe

11.

Zeitschriftenartikel

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), S. 3251 - 3275 (2023)

MPG.PuRe

12.

Zeitschriftenartikel

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), S. 2574 - 2589 (2023)

MPG.PuRe

13.

Zeitschriftenartikel

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)

MPG.PuRe

14.

Zeitschriftenartikel

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

MPG.PuRe

15.

Zeitschriftenartikel

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)

MPG.PuRe

16.

Zeitschriftenartikel

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)

MPG.PuRe

17.

Zeitschriftenartikel

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), S. 6259 - 6270 (2022)

MPG.PuRe

18.

Zeitschriftenartikel

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, S. 5385 - 5394 (2022)

MPG.PuRe

19.

Zeitschriftenartikel

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), S. 1691 - 1711 (2022)

MPG.PuRe

20.

Zeitschriftenartikel

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), S. 1172 - 1177 (2022)

MPG.PuRe

21.

Zeitschriftenartikel

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), S. 4147 - 4157 (2022)

MPG.PuRe

22.

Zeitschriftenartikel

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), S. 2548 - 2557 (2022)

MPG.PuRe

23.

Zeitschriftenartikel

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)

MPG.PuRe

24.

Zeitschriftenartikel

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)

MPG.PuRe

25.

Zeitschriftenartikel

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), S. 421 - 430 (2021)

MPG.PuRe

26.

Zeitschriftenartikel

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), S. 4241 - 4261 (2021)

MPG.PuRe

27.

Zeitschriftenartikel

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), S. 3195 - 3201 (2021)

MPG.PuRe

28.

Zeitschriftenartikel

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), S. 1922 - 1930 (2021)

MPG.PuRe

29.

Zeitschriftenartikel

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

MPG.PuRe

30.

Zeitschriftenartikel

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), S. 107 - 108 (2021)

MPG.PuRe

31.

Zeitschriftenartikel

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), S. 159 - 172 (2021)

MPG.PuRe

32.

Zeitschriftenartikel

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), S. 509 - 514 (2021)

MPG.PuRe

33.

Zeitschriftenartikel

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), S. 49 - 61 (2021)

MPG.PuRe

34.

Zeitschriftenartikel

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), S. 1237-1245 (2020)

MPG.PuRe

ZIP

35.

Zeitschriftenartikel

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)

MPG.PuRe

36.

Zeitschriftenartikel

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), S. 835 - 843 (2020)

MPG.PuRe

37.

Zeitschriftenartikel

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), S. 21014 - 21021 (2020)

MPG.PuRe

38.

Zeitschriftenartikel

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)

MPG.PuRe

39.

Zeitschriftenartikel

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

MPG.PuRe

40.

Zeitschriftenartikel

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), S. 601 - 633 (2020)

MPG.PuRe

41.

Zeitschriftenartikel

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), S. 1115 - 1123 (2020)

MPG.PuRe

42.

Zeitschriftenartikel

de Maré, S. W.; Venskutonytė, R.; Eltschkner, S.; de Groot, B. L.; Lindkvist-Petersson, K.: Structural basis for glycerol efflux and selectivity of human Aquaporin 7. Structure 28 (2), S. 215 - 222 (2020)

MPG.PuRe

ZIP

43.

Zeitschriftenartikel

Gapsys, V.; Perez-Benito, L.; Aldeghi, M.; Seeliger, D.; Van Vlijmen, H.; Tresadern, G.; de Groot, B. L.: Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science 11 (4), S. 1140 - 1152 (2020)

MPG.PuRe

44.

Zeitschriftenartikel

Smith, C. A.; Mazur, A.; Rout, A. K.; Becker, S.; Lee, D.; de Groot, B. L.; Griesinger, C.: Enhancing NMR derived ensembles with kinetics on multiple timescales. Journal of Biomolecular NMR 74 (1), S. 27 - 43 (2020)

MPG.PuRe

45.

Zeitschriftenartikel

Elisee, E.; Gapsys, V.; Mele, N.; Chaput, L.; Selwa, E.; de Groot, B. L.; Iorga, B. I.: Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design 33, S. 1031 - 1043 (2019)

MPG.PuRe

46.

Zeitschriftenartikel

Kopec, W.; Rothberg, B. S.; de Groot, B. L.: Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications 10, 5366 (2019)

MPG.PuRe

47.

Zeitschriftenartikel

Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B. L.; Grubmüller, H.: More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 40 (27), S. 2418 - 2431 (2019)

MPG.PuRe

48.

Zeitschriftenartikel

Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 5 (8), S. 1468 - 1474 (2019)

MPG.PuRe

49.

Zeitschriftenartikel

Öster, C.; Hendriks, K.; Kopec, W.; Chevelkov, V.; Shi, C.; Michl, D.; Lange, S.; Sun, H.; de Groot, B. L.; Lange, A.: The conduction pathway of potassium channels is water free under physiological conditions. Science Advances 5 (7), eaaw6756 (2019)

MPG.PuRe

50.

Zeitschriftenartikel

Gapsys, V.; de Groot, B. L.: Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8, e44718 (2019)

MPG.PuRe