Publications of the Department (MPG.PuRe list)

Journal Article (485)

1.
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 (2024)
2.
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)
3.
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 (2024)
4.
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)
5.
Journal Article
Clarke, A.; Farr, C. V.; El-Kasaby, A.; Szöllősi, D.; Freissmuth, M.; Sucic, S.; Stockner, T.: Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis. Protein Science 33 (1), e4842 (2024)
6.
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)
7.
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)
8.
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)
9.
Journal Article
Motycka, B.; Csarman, F.; Rupp, M.; Schnabel, K.; Nagy, G.; Karnpakdee, K.; Scheiblbrandner, S.; Tscheliessnig, R.; Oostenbrink, C.; Hammel, M. et al.; Ludwig, R.: Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase. ChemBioChem: A European Journal of Chemical Biology 24 (22), e202300431 (2023)
10.
Journal Article
Wilson, C.J.; Karttunen, M.; de Groot, B. L.; Gapsys, V.: Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. Journal of Chemical Theory and Computation 19 (21), pp. 7833 - 7845 (2023)
11.
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)
12.
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)
13.
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)
14.
Journal Article
Wiechers, H.; Kehl, A.; Hiller, M.; Eltzner, B.; Huckemann, S.F.; Meyer, A.; Tkach, I.; Bennati, M.; Pokern, Y.: Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra. Journal of Magnetic Resonance 353, 107491 (2023)
15.
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)
16.
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)
17.
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)
18.
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)
19.
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)
20.
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)
21.
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. The Journal of Biological Chemistry 299 (4), 103034 (2023)
22.
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)
23.
Journal Article
Wiechers, H.; Eltzner, B.; Mardia, K. V.; Huckemann, S. F.: Learning torus PCA-based classification for multiscale RNA correction with application to SARS-CoV-2. Journal of the Royal Statistical Society - Series C: Applied Statistics 72 (2), pp. 271 - 293 (2023)
24.
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)
25.
Journal Article
Dieball, C.; Godec, A.: Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. Physical Review Letters 130 (8), 087101 (2023)
26.
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)
27.
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)
28.
Journal Article
Hauke, L.; Primeßnig, A.; Eltzner, B.; Radwitz, J.; Huckemann, S. F.; Rehfeldt, F.: FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking. PLoS One 18 (2), e0279336 (2023)
29.
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)
30.
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)
31.
Journal Article
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)
32.
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)
33.
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)
34.
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)
35.
Journal Article
Dieball, C.; Godec, A.: Coarse graining empirical densities and currents in continuous-space steady states. Physical Review Research 4, 033243 (2022)
36.
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)
37.
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, pp. 5385 - 5394 (2022)
38.
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)
39.
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)
40.
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*, a. S.: Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases. ACS Central Science 8 (8), pp. 1091 - 1101 (2022)
41.
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)
42.
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)
43.
Journal Article
Bock, L. V.; Grubmüller, H.: Effects of cryo-EM cooling on structural ensembles. Nature Communications 13, 1709 (2022)
44.
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)
45.
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)
46.
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)
47.
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)
48.
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)
49.
Journal Article
Dieball, C.; Krapf, D.; Weiss, M.; Godec, A.: Scattering fingerprints of two-state dynamics. New Journal of Physics 24, 023004 (2022)
50.
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)
51.
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)
52.
Journal Article
Hartich, D.; Godec, A.: Emergent memory and kinetic hysteresis in strongly driven networks. Physical Review X 11 (4), 041047 (2021)
53.
Journal Article
Lapolla, A.; Godec, A.: BetheSF V2: 3-point propagator and additional external potentials. Computer Physics Communications 269, 108131 (2021)
54.
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)
55.
Journal Article
Blom, K.; Godec, A.: Criticality in cell adhesion. Physical Review X 11 (3), 031067 (2021)
56.
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)
57.
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)
58.
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)
59.
Journal Article
Hartich, D.; Godec, A.: Thermodynamic uncertainty relation bounds the extent of anomalous diffusion. Physical Review Letters 127 (8), 080601 (2021)
60.
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)
61.
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)
62.
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)
63.
Journal Article
Reinhardt, M.; Grubmüller, H.: GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. Computer Physics Communications 264, 107931 (2021)
64.
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)
65.
Journal Article
Lapolla, A.; Godec, A.: Toolbox for quantifying memory in dynamics along reaction coordinates. Physical Review Research 3 (2), L022018 (2021)
66.
Journal Article
Hett, T.; Zbik, T.; Mukherjee, S.; Matsuoka, H.; Bönigk, W.; Klose, D.; Rouillon, C.; Brenner, N.; Peuker, S.; Klement, R. et al.; Steinhoff, H.-J.; Grubmüller, H.; Seifert, R.; Schiemann, O.; Kaupp, U. B.: Spatiotemporal resolution of conformational changes in biomolecules by combining pulsed electron–electron double resonance spectroscopy with microsecond freeze-hyperquenching. Journal of the American Chemical Society 143 (18), pp. 6981 - 6989 (2021)
67.
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)
68.
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)
69.
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)
70.
Journal Article
Jahnke, K.; Grubmüller, H.; Igaev, M.; Göpfrich, K.: Choice of fluorophore affects dynamic DNA nanostructures. Nucleic Acids Research 49 (7), pp. 4186 - 4195 (2021)
71.
Journal Article
Heinz, L. P.; Grubmüller, H.: Per|Mut: Spatially resolved hydration entropies from atomistic simulations. Journal of Chemical Theory and Computation 17 (4), pp. 2090 - 2098 (2021)
72.
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)
73.
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)
74.
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)
75.
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)
76.
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)
77.
Journal Article
Risselada, H. J.; Grubmüller, H.: How proteins open fusion pores: insights from molecular simulations. European Biophysics Journal 50 (2), pp. 279 - 293 (2021)
78.
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)
79.
Journal Article
Lawson, C. L.; Kryshtafovych, A.; Adams, P. D.; Afonine, P. V.; Baker, M. L.; Barad, B. A.; Bond, P.; Burnley, T.; Cao, R.; Cheng, J. et al.; Chojnowski, G.; Cowtan, K.; Dill, K. A.; DiMaio, F.; Farrell, D. P.; Fraser, J. S.; Herzik Jr., M. A. H.; Hoh, S. W.; Hou, J.; Hung, L.-W.; Igaev, M.; Joseph, A. P.; Kihara, D.; Kumar, D.; Mittal, S.; Monastyrskyy, B.; Olek, M.; Palmer, C. M.; Patwardhan, A.; Perez, A.; Pfab, J.; Pintilie, G. D.; Richardson, J. S.; Rosenthal, P. B.; Sarkar, D.; Schäfer, L. U.; Schmid, M. F.; Schröder, G. F.; Shekhar, M.; Si, D.; Singharoy, A.; Terashi, G.; Terwilliger, T. C.; Vaiana, A.; Wang, L.; Wang, Z.; Wankowicz, S. A.; Williams, C. J.; Winn, M.; Wu, T.; Yu, X.; Zhang, K.; Berman, H. M.; Chiu, W.: Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods 18, pp. 156 - 164 (2021)
80.
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)
81.
Journal Article
Kohnke, B.; Kutzner, C.; Beckmann, A.; Lube, G.; Kabadshow, I.; Dachsel, H.; Grubmüller, H.: A CUDA fast multipole method with highly efficient M2L farfield evaluationfield evaluation. The International Journal of High Performance Computing Applications 35 (1), pp. 97 - 117 (2021)
82.
Journal Article
Lapolla, A.; Godec, A.: BetheSF: Efficient computation of the exact tagged-particle propagator in single-file systems via the Bethe eigenspectrum. Computer Physics Communications 258, 107569 (2021)
83.
Journal Article
Bubnis, G.; Grubmüller, H.: Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations. Biophysical Journal 119 (12), pp. 2418 - 2430 (2020)
84.
Journal Article
Kolar, M. H.; Bock, L. V.; Grubmüller, H.: Atomistic simulations of the human proteasome inhibited by a covalent ligand. arXiv, 2012.03387 (2020)
85.
Journal Article
Lapolla, A.; Hartich, D.; Godec, A.: Spectral theory of fluctuations in time-average statistical mechanics of reversible and driven systems. Physical Review Research 2 (4), 043084 (2020)
86.
Journal Article
Lapolla, A.; Godec, A.: Single-file diffusion in a bi-stable potential: Signatures of memory in the barrier-crossing of a tagged-particle. The Journal of Chemical Physics 153 (19), 194104 (2020)
87.
Journal Article
Kohnke, B.; Kutzner, C.; Grubmüller, H.: A GPU-accelerated fast multipole method for GROMACS: Performance and accuracy. Journal of Chemical Theory and Computation 16 (11), pp. 6938 - 6949 (2020)
88.
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)
89.
Journal Article
Reinhardt, M.; Grubmüller, H.: Variationally derived intermediates for correlated free-energy estimates between intermediate states. Physical Review E 102 (4), 043312 (2020)
90.
Journal Article
Lapolla, A.; Godec, A.: Faster uphill relaxation in thermodynamically equidistant temperature quenches. Physical Review Letters 125 (11), 110602 (2020)
91.
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)
92.
Journal Article
Igaev, M.; Grubmüller, H.: Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Computational Biology 16 (9), e1008132 (2020)
93.
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)
94.
Journal Article
Nagy, G.; Grubmueller, H.: How accurate is circular dichroism-based model validation? European Biophysics Journal 49 (6), pp. 497 - 510 (2020)
95.
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)
96.
Journal Article
Ukmar-Godec, T.; Fang, P.; Ibáñez de Opakua, A.; Henneberg, F.; Godec, A.; Pan, K. T.; Cima-Omori, M.-S.; Chari, A.; Mandelkow, E.; Urlaub, H. et al.; Zweckstetter, M.: Proteasomal degradation of the intrinsically disordered protein tau at single-residue resolution. Science Advances 6 (30), eaba3916 (2020)
97.
Journal Article
Reinhardt, M.; Grubmüller, H.: Determining free-energy differences through variationally derived intermediates. Journal of Chemical Theory and Computation 16 (6), pp. 3504 - 3512 (2020)
98.
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)
99.
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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