Publications of the Department (MPG.PuRe list)
Journal Article (492)
1.
Journal Article
Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models. Applied Spectroscopy (2024)
2.
Journal Article
57 (15), 155003 (2024)
Nonequilibrium statistical mechanics of money/energy exchange models. Journal of Physics A 3.
Journal Article
132 (14), 147101 (2024)
Emergence of Memory in Equilibrium versus Nonequilibrium Systems. Physical Review Letters 4.
Journal Article
15, 2431 (2024)
The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Nature Communications 5.
Journal Article
15, 2432 (2024)
RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nature Communications 6.
Journal Article
Resolving coupled pH titrations using alchemical free energy calculations. Journal of Computational Chemistry (2024)
7.
Journal Article
15, pp. 4960 - 4968 (2024)
Infrared spectroscopy reveals metal-independent carbonic anhydrase activity in crotonyl-CoA carboxylase/reductase. Chemical Science 8.
Journal Article
121 (7), e2319682121 (2024)
Molecular basis for human aquaporin inhibition. PNAS 9.
Journal Article
20 (2), pp. 914 - 925 (2024)
Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of Chemical Theory and Computation 10.
Journal Article
33 (1), e4842 (2024)
Probing binding and occlusion of substrate in the human creatine transporter-1 by computation and mutagenesis. Protein Science 11.
Journal Article
20, pp. 135 - 141 (2024)
Heating and cooling are fundamentally asymmetric and evolve along distinct pathways. Nature Physics 12.
Journal Article
63 (24), pp. 7807 - 7815 (2023)
Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation. Journal of Chemical Information and Modeling 13.
Journal Article
19 (22), pp. 8013 - 8019 (2023)
Why Solvent Response Contributions to Solvation Free Energies Are Compatible with Ben-Naim’s Theorem. Journal of Chemical Theory and Computation 14.
Journal Article
5 (4), L042030 (2023)
Asymmetric thermal relaxation in driven systems: Rotations go opposite ways. Physical Review Research 15.
Journal Article
24 (22), e202300431 (2023)
Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase. ChemBioChem: A European Journal of Chemical Biology 16.
Journal Article
19 (21), pp. 7833 - 7845 (2023)
Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. Journal of Chemical Theory and Computation 17.
Journal Article
29 (4), pp. 3141 - 3170 (2023)
Diffusion means in geometric spaces. Bernoulli 18.
Journal Article
19 (16), pp. 5516 - 5524 (2023)
Uncertainties in Markov State Models of Small Proteins. Journal of Chemical Theory and Computation 19.
Journal Article
5 (3), L032017 (2023)
Violation of local detailed balance upon lumping despite a clear timescale separation. Physical Review Research 20.
Journal Article
30, pp. 1380 - 1392 (2023)
Structural conservation of antibiotic interaction with ribosomes. Nature Structural & Molecular Biology 21.
Journal Article
353, 107491 (2023)
Bayesian optimization to estimate hyperfine couplings from 19F ENDOR spectra. Journal of Magnetic Resonance 22.
Journal Article
155 (8), e202213166 (2023)
Interactions between selectivity filter and pore helix control filter gating in the MthK channel. Journal of General Physiology 23.
Journal Article
19 (11), pp. 3251 - 3275 (2023)
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation 24.
Journal Article
19 (9), pp. 2574 - 2589 (2023)
Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. Journal of Chemical Theory and Computation 25.
Journal Article
52, pp. 361 - 390 (2023)
Simulation of Complex Biomolecular Systems: The Ribosome Challenge. Annual Review of Biophysics 26.
Journal Article
6, 82 (2023)
Automated relative binding free energy calculations from SMILES to ΔΔG. Communications Chemistry 27.
Journal Article
14 (1), 2178 (2023)
Central cavity dehydration as a gating mechanism of potassium channels. Nature Communications 28.
Journal Article
299 (4), 103034 (2023)
Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. The Journal of Biological Chemistry 29.
Journal Article
30, pp. 512 - 520 (2023)
Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel. Nature Structural and Molecular Biology 30.
Journal Article
72 (2), pp. 271 - 293 (2023)
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 31.
Journal Article
56 (15), 155002 (2023)
Feynman-Kac theory of time-integrated functionals: Itô versus functional calculus. Journal of Physics A 32.
Journal Article
130 (8), 087101 (2023)
Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. Physical Review Letters 33.
Journal Article
5 (1), 013135 (2023)
Thermodynamically consistent phase-field theory including nearest-neighbor pair correlations. Physical Review Research 34.
Journal Article
120 (8), e2215650120 (2023)
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 35.
Journal Article
18 (2), e0279336 (2023)
FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking. PLoS One 36.
Journal Article
14 (1), pp. 49 - 56 (2023)
Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories. The Journal of Physical Chemistry Letters 37.
Journal Article
131 (23), 237101 (2023)
Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime. Physical Review Letters 38.
Journal Article
13 (1), e1622 (2023)
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews: Computational Molecular Science 39.
Journal Article
55 (47), 475001 (2022)
On correlations and fluctuations of time-averaged densities and currents with general time-dependence. Journal of Physics A 40.
Journal Article
13 (1), 6810 (2022)
The 3D structure of lipidic fibrils of α-synuclein. Nature Communications 41.
Journal Article
129 (14), 140601 (2022)
Mathematical, thermodynamical, and experimental necessity for coarse graining empirical densities and currents in continuous space. Physical Review Letters 42.
Journal Article
4, 033243 (2022)
Coarse graining empirical densities and currents in continuous-space steady states. Physical Review Research 43.
Journal Article
18 (10), pp. 6259 - 6270 (2022)
Chemical Space Exploration with Active Learning and Alchemical Free Energies. Journal of Chemical Theory and Computation 44.
Journal Article
13, pp. 5385 - 5394 (2022)
The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nature Communications 45.
Journal Article
13, pp. 9668 - 9677 (2022)
Non-ergodicity of a globular protein extending beyond its functional timescale. Chemical Science 46.
Journal Article
20, pp. 2587 - 2599 (2022)
Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1. Computational and Structural Biotechnology Journal 47.
Journal Article
8 (8), pp. 1091 - 1101 (2022)
Intersubunit Coupling Enables Fast CO2-Fixation by Reductive Carboxylases. ACS Central Science 48.
Journal Article
105, 044404 (2022)
Estimating ruggedness of free-energy landscapes of small globular proteins from principal component analysis of molecular dynamics trajectories. Physical Review E 49.
Journal Article
62 (7), pp. 1691 - 1711 (2022)
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. Journal of Chemical Information and Modeling 50.
Journal Article
13, 1709 (2022)
Effects of cryo-EM cooling on structural ensembles. Nature Communications 51.
Journal Article
119 (12), e2115516119 (2022)
Bending-torsional elasticity and energetics of the plus-end microtubule tip. Proceedings of the National Academy of Sciences of the United States of America 52.
Journal Article
62 (5), pp. 1172 - 1177 (2022)
Pre-exascale computing of protein-ligand binding free energies with open source software for drug design. Journal of Chemical Information and Modeling 53.
Journal Article
144 (9), pp. 4147 - 4157 (2022)
Direct detection of bound ammonium ions in the selectivity filter of ion channels by solid-state NMR. Journal of the American Chemical Society 54.
Journal Article
50 (4), pp. 2258 - 2269 (2022)
Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel. Nucleic Acids Research 55.
Journal Article
65 (3), pp. 2548 - 2557 (2022)
Repositioning food and drug administration-approved drugs for inhibiting Biliverdin IXβ reductase B as a novel thrombocytopenia therapeutic target. Journal of Medicinal Chemistry 56.
Journal Article
24, 023004 (2022)
Scattering fingerprints of two-state dynamics. New Journal of Physics 57.
Journal Article
8 (3), eabk0627 (2022)
First-passage statistics of colloids on fractals: Theory and experimental realization. Science Advances 58.
Journal Article
13, 3792 (2022)
A litmus test for classifying recognition mechanisms of transiently binding proteins. Nature Communications 59.
Journal Article
11 (4), 041047 (2021)
Emergent memory and kinetic hysteresis in strongly driven networks. Physical Review X 60.
Journal Article
269, 108131 (2021)
BetheSF V2: 3-point propagator and additional external potentials. Computer Physics Communications 61.
Journal Article
104 (5), 054133 (2021)
Small-sample limit of the Bennett acceptance ratio method and the variationally derived intermediates. Physical Review E 62.
Journal Article
11 (3), 031067 (2021)
Criticality in cell adhesion. Physical Review X 63.
Journal Article
54 (35), 355601 (2021)
Time- and ensemble-average statistical mechanics of the Gaussian network model. Journal of Physics A 64.
Journal Article
266, 108022 (2021)
Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package. Computer Physics Communications 65.
Journal Article
17 (9), pp. 5766 - 5776 (2021)
Time-lagged independent component analysis of random walks and protein dynamics. Journal of Chemical Theory and Computation 66.
Journal Article
127 (8), 080601 (2021)
Thermodynamic uncertainty relation bounds the extent of anomalous diffusion. Physical Review Letters 67.
Journal Article
433 (17), 167002 (2021)
The persistent question of potassium channel permeation mechanisms. Journal of Molecular Biology 68.
Journal Article
120, pp. 3470 - 3482 (2021)
Spatially resolved free-energy contributions of native fold and molten-globule-like Crambin. Biophysical Journal 69.
Journal Article
12, 4466 (2021)
Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Nature Communications 70.
Journal Article
264, 107931 (2021)
GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. Computer Physics Communications 71.
Journal Article
12, 3606 (2021)
Tight docking of membranes before fusion represents a novel, metastable state with unique properties. Nature Communications 72.
Journal Article
3 (2), L022018 (2021)
Toolbox for quantifying memory in dynamics along reaction coordinates. Physical Review Research 73.
Journal Article
143 (18), pp. 6981 - 6989 (2021)
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 74.
Journal Article
4, 61 (2021)
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 75.
Journal Article
8 (3), pp. 421 - 430 (2021)
Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ 76.
Journal Article
125 (17), pp. 4241 - 4261 (2021)
Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations. Journal of Physical Chemistry B 77.
Journal Article
49 (7), pp. 4186 - 4195 (2021)
Choice of fluorophore affects dynamic DNA nanostructures. Nucleic Acids Research 78.
Journal Article
17 (4), pp. 2090 - 2098 (2021)
Per|Mut: Spatially resolved hydration entropies from atomistic simulations. Journal of Chemical Theory and Computation 79.
Journal Article
12 (12), pp. 3195 - 3201 (2021)
One plus one makes three: Triangular coupling of correlated amino acid mutations. Journal of Physical Chemistry Letters 80.
Journal Article
17 (3), pp. 1922 - 1930 (2021)
ATP-magnesium coordination: Protein structure-based force field evaluation and corrections. Journal of Chemical Theory and Computation 81.
Journal Article
50 (2), pp. 181 - 186 (2021)
Lipid–protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal 82.
Journal Article
50 (2), pp. 107 - 108 (2021)
Special issue: Multicomponent lipid membranes—how molecular organisation leads to function. European Biophysics Journal 83.
Journal Article
50 (2), pp. 159 - 172 (2021)
Structure, gating and interactions of the voltage-dependent anion channel. European Biophysics Journal 84.
Journal Article
50 (2), pp. 279 - 293 (2021)
How proteins open fusion pores: insights from molecular simulations. European Biophysics Journal 85.
Journal Article
590 (7846), pp. 509 - 514 (2021)
Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 86.
Journal Article
18, pp. 156 - 164 (2021)
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods 87.
Journal Article
35 (1), pp. 49 - 61 (2021)
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of Computer-Aided Molecular Design 88.
Journal Article
35 (1), pp. 97 - 117 (2021)
A CUDA fast multipole method with highly efficient M2L farfield evaluationfield evaluation. The International Journal of High Performance Computing Applications 89.
Journal Article
258, 107569 (2021)
BetheSF: Efficient computation of the exact tagged-particle propagator in single-file systems via the Bethe eigenspectrum. Computer Physics Communications 90.
Journal Article
119 (12), pp. 2418 - 2430 (2020)
Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations. Biophysical Journal 91.
Journal Article
Atomistic simulations of the human proteasome inhibited by a covalent ligand. arXiv, 2012.03387 (2020)
92.
Journal Article
2 (4), 043084 (2020)
Spectral theory of fluctuations in time-average statistical mechanics of reversible and driven systems. Physical Review Research 93.
Journal Article
153 (19), 194104 (2020)
Single-file diffusion in a bi-stable potential: Signatures of memory in the barrier-crossing of a tagged-particle. The Journal of Chemical Physics 94.
Journal Article
16 (11), pp. 6938 - 6949 (2020)
A GPU-accelerated fast multipole method for GROMACS: Performance and accuracy. Journal of Chemical Theory and Computation 95.
Journal Article
16 (11), p. 1237-1245 (2020)
Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine. Nature Chemical Biology 96.
Journal Article
102 (4), 043312 (2020)
Variationally derived intermediates for correlated free-energy estimates between intermediate states. Physical Review E 97.
Journal Article
125 (11), 110602 (2020)
Faster uphill relaxation in thermodynamically equidistant temperature quenches. Physical Review Letters 98.
Journal Article
9, e57589 (2020)
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 99.
Journal Article
16 (9), e1008132 (2020)
Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Computational Biology