Publications of the Department (MPG.PuRe list)

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)

MPG.PuRe

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)

MPG.PuRe

4.

Journal Article

Morgunova, E.; Nagy, G.; Yin, Y.; Zhu, F.; Nayak, S. P.; Xiao, T.; Sokolov, I.; Popov, A.; Laughton, C.; Grubmüller, H. et al.; Taipale, J.: Interfacial water confers transcription factors with dinucleotide specificity. Nature Structural & Molecular Biology 32, pp. 650 - 661 (2025)

MPG.PuRe

5.

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)

MPG.PuRe

6.

Journal Article

Blom, K.; Makarov, D. E.; Godec, A.: Hallmarks of deception in asset-exchange models. Physical Review Research 7, 013279 (2025)

MPG.PuRe

7.

Journal Article

Dieball, C.; Godec, A.: Perspective: Time irreversibility in systems observed at coarse resolution. The Journal of Chemical Physics 162, 090901 (2025)

MPG.PuRe

8.

Journal Article

Briand, E.; Kohnke, B.; Kutzner, C.; Grubmüller, H.: Constant pH Simulation with FMM Electrostatics in GROMACS. (A) Design and Applications. Journal of Chemical Theory and Computation 21 (4), pp. 1762 - 1786 (2025)

MPG.PuRe

9.

Journal Article

Kohnke, B.; Briand, E.; Kutzner, C.; Grubmüller, H.: Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation. Journal of Chemical Theory and Computation 21 (4), pp. 1787 - 1804 (2025)

MPG.PuRe

10.

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)

MPG.PuRe

11.

Journal Article

Dieball, C.; Mohebi Satalsari, Y.; Zuccolotto-Bernez, A. B.; Egelhaaf, S. U.; Escobedo-Sánchez, M. A.; Godec, A.: Precisely controlled colloids: a playground for path-wise non-equilibrium physics. Soft Matter 21 (11), pp. 2170 - 2181 (2025)

MPG.PuRe

12.

Journal Article

Blom, K.; Thiele, U.; Godec, A.: Local order controls the onset of oscillations in the nonreciprocal Ising model. Physical Review E 111 (2), 024207 (2025)

MPG.PuRe

13.

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)

MPG.PuRe

14.

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)

MPG.PuRe

15.

Journal Article

Tabanera-Bravo, J.; Godec, A.: Multiple Pareto-optimal solutions of the dissipation-adaptation trade-off. Physical Review Research 7, 013020 (2025)

MPG.PuRe

16.

Journal Article

Swarnkar, A.; Leidner, F.; Rout, A. K.; Ainatzi, S.; Schmidt, C. C.; Becker, S.; Urlaub, H.; Griesinger, C.; Grubmüller, H.; Stein, A.: Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes. The EMBO Journal 43 (24), pp. 6705 - 6739 (2024)

MPG.PuRe

17.

Journal Article

Rennekamp, B.; Grubmüller, H.; Gräter, F.: Hidden length lets collagen buffer mechanical and chemical stress. Physical Review E 110, 054408 (2024)

MPG.PuRe

18.

Journal Article

Goswami, K.; Cherstvy, A. G.; Godec, A.; Metzler, R.: Anomalous diffusion of active Brownian particles in responsive elastic gels: Nonergodicity, non-Gaussianity, and distributions of trapping times. Physical Review E 110, 044609 (2024)

MPG.PuRe

19.

Journal Article

Schultze, S.; Grubmüller, H.: Bayesian electron density determination from sparse and noisy single-molecule X-ray scattering images. Science Advances 10 (43), eadp4425 (2024)

MPG.PuRe

20.

Journal Article

Hartich, D.; Godec, A.: Comment on “Inferring broken detailed balance in the absence of observable currents”. Nature Communications 15, 8678 (2024)

MPG.PuRe

21.

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)

MPG.PuRe

22.

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)

MPG.PuRe

23.

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)

MPG.PuRe

24.

Journal Article

Nagy, G.; Hoffmann, S. V.; Jones, N. C.; Grubmüller, H.: Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models. Applied Spectroscopy 78 (9), pp. 897 - 911 (2024)

MPG.PuRe

25.

Journal Article

Vollmar, L.; Bebon, R.; Schimpf, J.; Flietel, B.; Celiksoy, S.; Sönnichsen, C.; Godec, A.; Hugel, T.: Model-free inference of memory in conformational dynamics of a multi-domain protein. Journal of Physics A 57 (36), 365001 (2024)

MPG.PuRe

26.

Journal Article

Dieball, C.; Godec, A.: Thermodynamic Bounds on Generalized Transport: From Single-Molecule to Bulk Observables. Physical Review Letters 133 (6), 067101 (2024)

MPG.PuRe

27.

Journal Article

Konold, P. E.; Monrroy, L.; Bellisario, A.; Filipe, D.; Adams, P.; Alvarez, R.; Bean, R.; Bielecki, J.; Bódizs, S.; Ducrocq, G. et al.; Grubmüller, H.; Kirian, R. A.; Kloos, M.; Koliyadu, J. C. P.; Koua, F. H. M.; Larkiala, T.; Letrun, R.; Lindsten, F.; Maihöfer, M.; Martin, A. V.; Mészáros, P.; Mutisya, J.; Nimmrich, A.; Okamoto, K.; Round, A.; Sato, T.; Valerio, J.; Westphal, D.; Wollter, A.; Yenupuri, T. V.; You, T.; Maia, F.; Westenhoff, S.: Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs. Nature Methods 21, pp. 1608 - 1611 (2024)

MPG.PuRe

28.

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)

MPG.PuRe

29.

Journal Article

Dunlop, J.; Cerisola, F.; Tabanera-Bravo, J.; Anders, J.: Thermodynamically optimal protocols for dual-purpose qubit operations. Physical Review Research 6 (3), 033005 (2024)

MPG.PuRe

30.

Journal Article

Lawson, C. L.; Kryshtafovych, A.; Pintilie, G. D.; Burley, S. K.; Černý, J.; Chen, V. B.; Emsley, P.; Gobbi, A.; Joachimiak, A.; Noreng, S. et al.; Prisant, M. G.; Read, R. J.; Richardson, J. S.; Rohou, A. L.; Schneider, B.; Sellers, B. D.; Shao, C.; Sourial, E.; Williams, C. I.; Williams, C. J.; Yang, Y.; Abbaraju, V.; Afonine, P. V.; Baker, M. L.; Bond, P. S.; Blundell, T. L.; Burnley, T.; Campbell, A.; Cao, R.; Cheng, J.; Chojnowski, G.; Cowtan, K. D.; DiMaio, F.; Esmaeeli, R.; Giri, N.; Grubmüller, H.; Hoh, S. W.; Hou, J.; Hryc, C. F.; Hunte, C.; Igaev, M.; Joseph, A. P.; Kao, W.-C.; Kihara, D.; Kumar, D.; Lang, L.; Lin, S.; Subramaniya, S. R. M. V.; Mittal, S.; Mondal, A.; Moriarty, N. W.; Muenks, A.; Murshudov, G. N.; Nicholls, R. A.; Olek, M.; Palmer, C. M.; Perez, A.; Pohjolainen, E.; Pothula, K. R.; Rowley, C. N.; Sarkar, D.; Schäfer, L. U.; Schlicksup, C. J.; Schröder, G. F.; Shekhar, M.; Si, D.; Singharoy, A.; Sobolev, O. V.; Terashi, G.; Vaiana, A. C.; Vedithi, S. C.; Verburgt, J.; Wang, X.; Warshamanage, R.; Winn, M. D.; Weyand, S.; Yamashita, K.; Zhao, M.; Schmid, M. F.; Berman, H. M.; Chiu, W.: Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature Methods 21, pp. 1340 - 1348 (2024)

MPG.PuRe

31.

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)

MPG.PuRe

32.

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)

MPG.PuRe

33.

Journal Article

Bock, L. V.; Igaev, M.; Grubmüller, H.: Single-particle Cryo-EM and molecular dynamics simulations: A perfect match. Current Opinion in Structural Biology 86, 102825 (2024)

MPG.PuRe

34.

Journal Article

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), pp. 1445 - 1470 (2024)

MPG.PuRe

35.

Journal Article

Lauer, S.M.; Reepmeyer, M.; Berendes, O.; Klepacki, D.; Gasse, J.; Gabrielli, S.; Grubmüller, H.; Bock, L. V.; Krizsan, A.; Nikolay, R. et al.; Spahn, C.M.T.; Hoffmann, R.: Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88. Nature Communications 15, 3945 (2024)

MPG.PuRe

36.

Journal Article

Blom, K.; Song, K.; Vouga, E.; Godec, A.; Makarov, D. E.: Milestoning estimators of dissipation in systems observed at a coarse resolution. PNAS 121 (17), e2318333121 (2024)

MPG.PuRe

37.

Journal Article

Miao, M.; Makarov, D. E.; Blom, K.: Nonequilibrium statistical mechanics of money/energy exchange models. Journal of Physics A 57 (15), 155003 (2024)

MPG.PuRe

38.

Journal Article

Zhao, X.; Hartich, D.; Godec, A.: Emergence of Memory in Equilibrium versus Nonequilibrium Systems. Physical Review Letters 132 (14), 147101 (2024)

MPG.PuRe

39.

Journal Article

Gersteuer, F.; Morici, M.; Gabrielli, S.; Fujiwara, K.; Safdari, H. A.; Paternoga, H.; Bock, L. V.; Chiba, S.; Wilson, D. N.: The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Nature Communications 15, 2431 (2024)

MPG.PuRe

Full

40.

Journal Article

Morici, M.; Gabrielli, S.; Fujiwara, K.; Paternoga, H.; Beckert, B.; Bock, L. V.; Chiba, S.; Wilson, D. N.: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nature Communications 15, 2432 (2024)

MPG.PuRe

41.

Journal Article

Gomez, A.; Tinzl, M.; Stoffel, G.; Westedt, H.; Grubmüller, H.; Erb, T.J.; Vöhringer-Martinez, E.; Stripp, S.T.: Infrared spectroscopy reveals metal-independent carbonic anhydrase activity in crotonyl-CoA carboxylase/reductase. Chemical Science 15, pp. 4960 - 4968 (2024)

MPG.PuRe

42.

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)

MPG.PuRe

43.

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)

MPG.PuRe

44.

Journal Article

Ibáñez, M.; Dieball, C.; Lasanta, A.; Godec, A.; Rica, R. A.: Heating and cooling are fundamentally asymmetric and evolve along distinct pathways. Nature Physics 20, pp. 135 - 141 (2024)

MPG.PuRe

45.

Journal Article

Gomez, A.; Erb, T. J.; Grubmüller, H.; Vöhringer-Martinez, E.: Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO₂ Fixation. Journal of Chemical Information and Modeling 63 (24), pp. 7807 - 7815 (2023)

MPG.PuRe

46.

Journal Article

Heinz, L.; Grubmüller, H.: Why Solvent Response Contributions to Solvation Free Energies Are Compatible with Ben-Naim’s Theorem. Journal of Chemical Theory and Computation 19 (22), pp. 8013 - 8019 (2023)

MPG.PuRe

47.

Journal Article

Dieball, C.; Wellecke, G.; Godec, A.: Asymmetric thermal relaxation in driven systems: Rotations go opposite ways. Physical Review Research 5 (4), L042030 (2023)

MPG.PuRe

48.

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)

MPG.PuRe

49.

Journal Article

Kozlowski, N.; Grubmüller, H.: Uncertainties in Markov State Models of Small Proteins. Journal of Chemical Theory and Computation 19 (16), pp. 5516 - 5524 (2023)

MPG.PuRe

50.

Journal Article

Hartich, D.; Godec, A.: Violation of local detailed balance upon lumping despite a clear timescale separation. Physical Review Research 5 (3), L032017 (2023)

MPG.PuRe

51.

Journal Article

Paternoga, H.; Crowe-McAuliffe, C.; Bock, L. V.; Koller, T. O.; Morici, M.; Beckert, B.; Myasnikov, A. G.; Grubmüller, H.; Nováček, J.; Wilson, D. N.: Structural conservation of antibiotic interaction with ribosomes. Nature Structural & Molecular Biology 30, pp. 1380 - 1392 (2023)

MPG.PuRe

52.

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)

MPG.PuRe

53.

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)

MPG.PuRe

54.

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)

MPG.PuRe

55.

Journal Article

Bock, L. V.; Gabrielli, S.; Kolář, M. H.; Grubmüller, H.: Simulation of Complex Biomolecular Systems: The Ribosome Challenge. Annual Review of Biophysics 52, pp. 361 - 390 (2023)

MPG.PuRe

56.

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)

MPG.PuRe

57.

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)

MPG.PuRe

58.

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)

MPG.PuRe

59.

Journal Article

Pan, Y.; Pohjolainen, E.; Schmidpeter, P. A. M.; Vaiana, A. C.; Nimigean, C. M.; Grubmüller, H.; Scheuring, S.: Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel. Nature Structural and Molecular Biology 30, pp. 512 - 520 (2023)

MPG.PuRe

60.

Journal Article

Dieball, C.; Godec, A.: Feynman-Kac theory of time-integrated functionals: Itô versus functional calculus. Journal of Physics A 56 (15), 155002 (2023)

MPG.PuRe

61.

Journal Article

Dieball, C.; Godec, A.: Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. Physical Review Letters 130 (8), 087101 (2023)

MPG.PuRe

62.

Journal Article

Blom, K.; Ziethen, N.; Zwicker, D.; Godec, A.: Thermodynamically consistent phase-field theory including nearest-neighbor pair correlations. Physical Review Research 5 (1), 013135 (2023)

MPG.PuRe

63.

Journal Article

Badocha, M.; Wieczór, M.; Marciniak, A.; Kleist, C.; Grubmüller, H.; Czub, J.: Molecular mechanism and energetics of coupling between substrate binding and product release in the F₁-ATPase catalytic cycle. Proceedings of the National Academy of Sciences of the United States of America 120 (8), e2215650120 (2023)

MPG.PuRe

64.

Journal Article

Godec, A.; Makarov, D. E.: Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories. The Journal of Physical Chemistry Letters 14 (1), pp. 49 - 56 (2023)

MPG.PuRe

65.

Journal Article

Bebon, R.; Godec, A.: Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime. Physical Review Letters 131 (23), 237101 (2023)

MPG.PuRe

66.

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)

MPG.PuRe

67.

Journal Article

Dieball, C.; Godec, A.: On correlations and fluctuations of time-averaged densities and currents with general time-dependence. Journal of Physics A 55 (47), 475001 (2022)

MPG.PuRe

68.

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)

MPG.PuRe

69.

Journal Article

Dieball, C.; Godec, A.: Mathematical, thermodynamical, and experimental necessity for coarse graining empirical densities and currents in continuous space. Physical Review Letters 129 (14), 140601 (2022)

MPG.PuRe

70.

Journal Article

Dieball, C.; Godec, A.: Coarse graining empirical densities and currents in continuous-space steady states. Physical Review Research 4, 033243 (2022)

MPG.PuRe

71.

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)

MPG.PuRe

72.

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)

MPG.PuRe

73.

Journal Article

Li, J.; Xie, J.; Godec, A.; Weninger, K.; Liu, C.; Smith, J.; Hong, L.: Non-ergodicity of a globular protein extending beyond its functional timescale. Chemical Science 13, pp. 9668 - 9677 (2022)

MPG.PuRe

74.

Journal Article

Padányi, R.; Farkas, B.; Tordai, H.; Kiss, B.; Grubmüller, H.; Soya, N.; Lukács, G.; Kellermayer, M.; Hegedus, T.: Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1. Computational and Structural Biotechnology Journal 20, pp. 2587 - 2599 (2022)

MPG.PuRe

75.

Journal Article

DeMirci, H.; Rao, Y.; Stoffel, G. M.; Vögeli, B.; Schell, K.; Gomez, A.; Batyuk, A.; Gati, C.; Sierra, R. G.; Hunter, M. S. et al.; Dao, E. H.; Ciftci, H. I.; Hayes, B.; Poitevin, F.; Li, P.-N.; Kaur, M.; Tono, K.; Saez, D. A.; Deutsch, S.; Yoshikuni, Y.; Grubmüller, H.; Erb, T. J.; Vöhringer-Martinez, E.; Wakatsuki, S.: Intersubunit Coupling Enables Fast CO₂-Fixation by Reductive Carboxylases. ACS Central Science 8 (8), pp. 1091 - 1101 (2022)

MPG.PuRe

76.

Journal Article

Volkhardt, A.; Grubmüller, H.: Estimating ruggedness of free-energy landscapes of small globular proteins from principal component analysis of molecular dynamics trajectories. Physical Review E 105, 044404 (2022)

MPG.PuRe

77.

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)

MPG.PuRe

78.

Journal Article

Bock, L. V.; Grubmüller, H.: Effects of cryo-EM cooling on structural ensembles. Nature Communications 13, 1709 (2022)

MPG.PuRe

79.

Journal Article

Igaev, M.; Grubmüller, H.: Bending-torsional elasticity and energetics of the plus-end microtubule tip. Proceedings of the National Academy of Sciences of the United States of America 119 (12), e2115516119 (2022)

MPG.PuRe

80.

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)

MPG.PuRe

81.

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)

MPG.PuRe

82.

Journal Article

Kolar, M. H.; Nagy, G.; Kunkel, J.; Vaiana, S. M.; Bock, L. V.; Grubmüller, H.: Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel. Nucleic Acids Research 50 (4), pp. 2258 - 2269 (2022)

MPG.PuRe

83.

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)

MPG.PuRe

84.

Journal Article

Dieball, C.; Krapf, D.; Weiss, M.; Godec, A.: Scattering fingerprints of two-state dynamics. New Journal of Physics 24, 023004 (2022)

MPG.PuRe

85.

Journal Article

Zunke, C.; Bewerunge, J.; Platten, F.; Egelhaaf , S. U.; Godec, A.: First-passage statistics of colloids on fractals: Theory and experimental realization. Science Advances 8 (3), eabk0627 (2022)

MPG.PuRe

86.

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)

MPG.PuRe

87.

Journal Article

Hartich, D.; Godec, A.: Emergent memory and kinetic hysteresis in strongly driven networks. Physical Review X 11 (4), 041047 (2021)

MPG.PuRe

88.

Journal Article

Lapolla, A.; Godec, A.: BetheSF V2: 3-point propagator and additional external potentials. Computer Physics Communications 269, 108131 (2021)

MPG.PuRe

89.

Journal Article

Reinhardt, M.; Grubmüller, H.: Small-sample limit of the Bennett acceptance ratio method and the variationally derived intermediates. Physical Review E 104 (5), 054133 (2021)

MPG.PuRe

90.

Journal Article

Blom, K.; Godec, A.: Criticality in cell adhesion. Physical Review X 11 (3), 031067 (2021)

MPG.PuRe

91.

Journal Article

Lapolla, A.; Vossel, M.; Godec, A.: Time- and ensemble-average statistical mechanics of the Gaussian network model. Journal of Physics A 54 (35), 355601 (2021)

MPG.PuRe

92.

Journal Article

Nagy, G.; Grubmüller, H.: Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package. Computer Physics Communications 266, 108022 (2021)

MPG.PuRe

93.

Journal Article

Schultze, S.; Grubmüller, H.: Time-lagged independent component analysis of random walks and protein dynamics. Journal of Chemical Theory and Computation 17 (9), pp. 5766 - 5776 (2021)

MPG.PuRe

94.

Journal Article

Hartich, D.; Godec, A.: Thermodynamic uncertainty relation bounds the extent of anomalous diffusion. Physical Review Letters 127 (8), 080601 (2021)

MPG.PuRe

95.

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)

MPG.PuRe

96.

Journal Article

Heinz, L. P.; Grubmüller, H.: Spatially resolved free-energy contributions of native fold and molten-globule-like Crambin. Biophysical Journal 120, pp. 3470 - 3482 (2021)

MPG.PuRe

97.

Journal Article

Beckert, B.; Leroy, E. C.; Sothiselvam, S.; Bock, L. V.; Svetlov, M. S.; Graf, M.; Arenz, S.; Abdelshahid, M.; Seip, B.; Grubmüller, H. et al.; Mankin, A. S.; Innis, C. A.; Vàzquez-Laslop, N.; Wilson, D. N.: Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Nature Communications 12, 4466 (2021)

MPG.PuRe

98.

Journal Article

Reinhardt, M.; Grubmüller, H.: GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. Computer Physics Communications 264, 107931 (2021)

MPG.PuRe

99.

Journal Article

Witkowska, A.; Heinz, L. P.; Grubmüller, H.; Jahn, R.: Tight docking of membranes before fusion represents a novel, metastable state with unique properties. Nature Communications 12, 3606 (2021)

MPG.PuRe