Publications of the Department (MPG.PuRe list)

1.

Journal Article

Schmidt, L.; Kopec, W.: Deep learning as a generator of sodium channel state hypotheses. Journal of General Physiology 158 (3), e202513938 (2026)

MPG.PuRe

DOI

2.

Journal Article

Kalutskii, M.; Wilson, C. J.; Grubmüller, H.; Igaev, M.: Improving Conformational Ensembles of Folded Proteins in Go̅Martini. Journal of Chemical Theory and Computation 22 (5), pp. 2369 - 2379 (2026)

MPG.PuRe

DOI

3.

Journal Article

Schäffner, M.; Smith, C. A.; Tampé, R.; Grubmüller, H.: Braess’ Paradox in Enzyme Kinetics: Asymmetry from Population Balance without Direct Cooperativity. Journal of Chemical Theory and Computation 22 (4), pp. 1982 - 1999 (2026)

MPG.PuRe

DOI

4.

Journal Article

Schultze, S.; Grubmüller, H.: Bayesian MINFLUX Localization Microscopy. ACS Photonics 13 (3), pp. 833 - 837 (2026)

MPG.PuRe

DOI

publisher-version

5.

Journal Article

Bied, M.; Landra-Willm, A.; Chassot, A. A.; Mendez-Otalvaro, E. F.; Sueur, B.; Roßmann, K.; de la Peña, E.; Fossat, P.; Tucker, S. J.; Noël, J. et al.; Kopec, W.; Viana, F.; Broichhagen, J.; Boué-Grabot, E.; Sandoz, G.: Light-induced analgesia provides a drug-free optical method for pain relief via activation of TRAAK k⁺ channels. Nature Communications 17, 620 (2026)

MPG.PuRe

DOI

publisher-version

6.

Journal Article

Blom, K.; Thiele, U.; Godec, A.: Dynamic models for two nonreciprocally coupled fields: A microscopic derivation for zero, one, and two conservation laws. SciPost Physics 20, 005 (2026)

MPG.PuRe

DOI

publisher-version

7.

Journal Article

Xu, A. M.; Szöllősi, D.; Grubmüller, H.; Regev, O.: Large Data Set Analysis Reveals Structural Origin of Peptide Collisional Cross Section Bimodal Behavior. Journal of the American Society for Mass Spectrometry 37 (1), pp. 279 - 288 (2026)

MPG.PuRe

DOI

publisher-version

8.

Journal Article

Mendez-Otalvaro, E.; Kopec, W.; Schewe, M.; de Groot, B. L.: One pocket to activate them all (?): Efforts on understanding the modulator pocket in K2P channels. Channels 20 (1), 2602975 (2026)

MPG.PuRe

DOI

publisher-version

9.

Journal Article

Huang, P.; Venskutonytė, R.; Wilson, C. J.; Bsharat, S.; Prasad, R. B.; Gourdon, P.; Artner, I.; de Groot, B. L.; Lindkvist-Petersson, K.: Structural insights into AQP3 channel closure upon pH and redox changes reveal an autoregulatory molecular mechanism. Nature Communications 16, 10997 (2025)

MPG.PuRe

DOI

publisher-version

10.

Journal Article

Öster, C.; de Vries, R.; Li, J.; Qoraj, D.; Lange, S.; Shi, C.; Kopec, W.; de Groot, B. L.; Lange, A.: Atomistic Mechanism of Calcium-Mediated Inward Rectification of the MthK Potassium Channel by Solid-State NMR and MD Simulations. Journal of the American Chemical Society 147 (49), pp. 45536 - 45548 (2025)

MPG.PuRe

DOI

publisher-version

11.

Journal Article

Zhao, X.; Makarov, D. E.; Godec, A.: Towards Markov-state holography. New Journal of Physics 27, 125002 (2025)

MPG.PuRe

DOI

publisher-version

12.

Journal Article

Behera, S.; Gapsys, V.; de Groot, B. L.: Evaluation of the ABCG2 Charge Model in Protein–Ligand Binding Free-Energy Calculations. Journal of Chemical Information and Modeling 65 (21), pp. 11505 - 11509 (2025)

MPG.PuRe

DOI

publisher-version

13.

Journal Article

Chen, H.; Cretu, C.; Trebilcock, A.; Evdokimova, N.; Babai, N.; Feldmann, L.; Leidner, F.; Benseler, F.; Mutschall, S.; Esch, K. et al.; Szabo, C. Z. K.; Pena, V.; Pape, C.; Grubmüller, H.; Strenzke, N.; Brose, N.; Wichmann, C.; Preobraschenski, J.; Moser, T.: Structure and function of otoferlin, a synaptic protein of sensory hair cells essential for hearing. Science Advances 11 (42), eady8532 (2025)

MPG.PuRe

DOI

publisher-version

14.

Journal Article

Vrentzou, A.; Leidner, F.; Schmidt, C. C.; Grubmüller, H.; Stein, A.: UBE2J2 sensitizes the ERAD ubiquitination cascade to changes in membrane lipid saturation. Nature Communications 16, 8973 (2025)

MPG.PuRe

DOI

publisher-version

15.

Journal Article

Otteson, L.; Nagy, G.; Kunkel, J.; Kodis, G.; Bock, L. V.; Bignon, C.; Longhi, S.; Zheng, W.; Grubmüller, H.; Vaiana, A. C. et al.; Vaiana, S. M.: Transient non-local interactions dominate the dynamics of measles virus N_TAIL. Communications Chemistry 8, 298 (2025)

MPG.PuRe

DOI

publisher-version

16.

Journal Article

Han, M.; Frieg, B.; Matthes, D.; Leonov, A.; Ryazanov, S.; Giller, K.; Nimerovsky, E.; Stampolaki, M.; Xue, K.; Overkamp, K. et al.; Dienemann, C.; Riedel, D.; Giese, A.; Becker, S.; de Groot, B. L.; Schröder, G. F.; Andreas, L. B.; Griesinger, C.: Anle138b binds predominantly to the central cavity in lipidic Aβ₄₀ fibrils and modulates fibril formation. Nature Communications 16, 8850 (2025)

MPG.PuRe

DOI

publisher-version

17.

Journal Article

Orth, B.; Pohl, P.; Aust, F.; Ji, Y.; Seenivasan, A.; Dybkov, O.; Liang, X. J.; Bock, L.; Leidner, F.; Levantovsky, S. et al.; Schardey, P.; Sander, P.; Disch, N. J.; Trautz, M. L.; Mizi, A.; Papantonis, A.; Lenz, C.; Grubmüller, H.; Steinchen, W.; Behrends, C.; Urlaub, H.; Gehringer, M.; Lorenz, S.: Selective ubiquitination of drug-like small molecules by the ubiquitin ligase HUWE1. Nature Communications 16, 8182 (2025)

MPG.PuRe

DOI

publisher-version

18.

Journal Article

Kudalkar, G. P.; Leidner, F.; Kumar, N.; Hass, J. L.; Madzelan, P.; Powell, D. R.; Day, V. W.; Magueres, P. L.; Ferrara, J. D.; Daniels, L. M. et al.; Yamano, A.; Ito, S.; Niu, W.; Grubmüller, H.; Wilson, M. A.; Berkowitz, D. B.: Is a Malleable Active Site Loop the Key to High Substrate Promiscuity? Hybrid, Biocatalytic Route to Structurally Diverse Taxoid Side Chains with Remarkable Dual Stereocontrol. Angewandte Chemie International Edition 64 (36), e202510889 (2025)

MPG.PuRe

DOI

publisher-version

19.

Journal Article

Schultze, S.; Luke, D. R.; Grubmüller, H.: Structure Determination from Single-Molecule X-ray Scattering Images Using Stochastic Gradient Ascent. Journal of Chemical Theory and Computation 21 (16), pp. 8227 - 8234 (2025)

MPG.PuRe

DOI

publisher-version

20.

Journal Article

Szöllősi, D.; Pratihar, S.; Mukhopadhyay, D.; Rout, A. K.; Reddy, G. J.; Ebersberger, N.; Becker, S.; Nagy, G.; Rauscher, S.; Lee, D. et al.; Klement, R.; Griesinger, C.; Grubmüller, H.: Hierarchically ordered multi-timescale structural dynamics of the intrinsically disordered p53 transactivation domain. bioRxiv (2025)

MPG.PuRe

DOI

21.

Journal Article

Behera, S.; Hahn, D. F.; Wilson, C. J.; Marsili, S.; Tresadern, G.; Gapsys, V.; de Groot, B. L.: Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy. Journal of Chemical Information and Modeling 65 (13), pp. 6927 - 6938 (2025)

MPG.PuRe

DOI

publisher-version

22.

Journal Article

Dunlop, J.; Cerisola, F.; Monsel, J.; Sevitz, S.; Tabanera-Bravo, J.; Dexter, J.; Fedele, F.; Ares, N.; Anders, J.: Extra cost of erasure due to quantum lifetime broadening. Physical Review A 112 (1), L010601 (2025)

MPG.PuRe

DOI

publisher-version

23.

Journal Article

Rogacheva, O. N.; Kopec, W.: Asymmetric Nature of MscL Opening Revealed by Molecular Dynamics Simulations. Journal of Chemical Information and Modeling 65 (12), pp. 6129 - 6143 (2025)

MPG.PuRe

DOI

publisher-version

24.

Journal Article

Vossel, M.; de Groot, B. L.; Godec, A.: Allosteric Lever: Toward a Principle of Specific Allosteric Response. Physical Review X 15 (2), 021097 (2025)

MPG.PuRe

DOI

publisher-version

25.

Journal Article

Dieball, C.; Godec, A.: Thermodynamic correlation inequalities for finite times and transients. Journal of Physics A 58 (25), 255001 (2025)

MPG.PuRe

DOI

publisher-version

26.

Journal Article

Kalutskii, M.; Grubmüller, H.; Volkov, V. A.; Igaev, M.: Microtubule dynamics are defined by conformations and stability of clustered protofilaments. Proceedings of the National Academy of Sciences of the United States of America 122 (22), e2424263122 (2025)

MPG.PuRe

DOI

27.

Journal Article

Hui, C.; de Vries, R.; Kopec, W.; de Groot, B. L.: Effective polarization in potassium channel simulations: Ion conductance, occupancy, voltage response, and selectivity. Proceedings of the National Academy of Sciences of the United States of America 122 (21), e2423866122 (2025)

MPG.PuRe

DOI

publisher-version

28.

Journal Article

Loos, S. A. M.; Godec, A.: Non-Markovian effects in nonequilibrium systems. Journal of Physics A 58 (22), 220301 (2025)

MPG.PuRe

DOI

publisher-version

29.

Journal Article

Schmidt, L.; de Groot, B. L.: Identification of allosteric sites and ligand-induced modulation in the dopamine receptor through large-scale alchemical mutation scan. Chemical Science 16, pp. 9357 - 9365 (2025)

MPG.PuRe

DOI

publisher-version

30.

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

DOI

publisher-version

31.

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

DOI

publisher-version

32.

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

DOI

33.

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

DOI

publisher-version

34.

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

DOI

35.

Journal Article

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

MPG.PuRe

DOI

publisher-version

36.

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

DOI

publisher-version

37.

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

DOI

publisher-version

38.

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

DOI

publisher-version

39.

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

DOI

publisher-version

40.

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

DOI

publisher-version

41.

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

DOI

publisher-version

42.

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

DOI

43.

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

DOI

publisher-version

44.

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

DOI

publisher-version

45.

Journal Article

Lee, S.-J.; Schillings, J.; de Vries, R.; Matamoros, M.; de Groot, B. L.; Nichols, C. G.: From selective permeation to physiology in potassium channels. Function 6 (6), zqaf050 (2025)

MPG.PuRe

DOI

publisher-version

46.

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

DOI

publisher-version

47.

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

DOI

48.

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

DOI

49.

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

DOI

publisher-version

50.

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

DOI

publisher-version

51.

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

DOI

publisher-version

52.

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

DOI

publisher-version

53.

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

DOI

publisher-version

54.

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

DOI

publisher-version

55.

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

DOI

publisher-version

56.

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

DOI

publisher-version

57.

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

DOI

publisher-version

58.

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

DOI

publisher-version

59.

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

DOI

publisher-version

60.

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

DOI

61.

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

DOI

publisher-version

62.

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

DOI

publisher-version

pre-print

63.

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

DOI

publisher-version

64.

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

DOI

65.

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

DOI

publisher-version

66.

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

DOI

publisher-version

67.

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

DOI

publisher-version

68.

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

DOI

publisher-version

69.

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

DOI

Full

publisher-version

70.

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

DOI

publisher-version

71.

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

DOI

publisher-version

72.

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

DOI

publisher-version

73.

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

DOI

publisher-version

74.

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

DOI

publisher-version

75.

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

DOI

76.

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

DOI

publisher-version

77.

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

DOI

publisher-version

78.

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

DOI

publisher-version

79.

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

DOI

publisher-version

80.

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

DOI

publisher-version

81.

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

DOI

publisher-version

82.

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

DOI

publisher-version

83.

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

DOI

publisher-version

84.

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

DOI

publisher-version

85.

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

DOI

publisher-version

86.

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

DOI

publisher-version

87.

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

DOI

publisher-version

88.

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

DOI

publisher-version

89.

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

DOI

90.

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

DOI

publisher-version

91.

Journal Article

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

MPG.PuRe

DOI

publisher-version

92.

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

DOI

publisher-version

93.

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

DOI

publisher-version

94.

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

DOI

95.

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

DOI

publisher-version

96.

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

DOI

97.

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

DOI

publisher-version

pre-print

98.

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

DOI

publisher-version

99.

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

DOI

publisher-version

pre-print

Publications of the Department (MPG.PuRe list)

Journal Article (550)