Publications of the Department (MPG.PuRe list)
Journal Article (433)
1.
Journal Article
Inter-subunit coupling enables fast CO2-fixation by reductive carboxylases. ACS Central Science, In Press (2022)
2.
Journal Article
62 (7), pp. 1691 - 1711 (2022)
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. Journal of Chemical Infomation and Modeling 3.
Journal Article
24 (2), 023004 (2022)
Scattering fingerprints of two-state dynamics. New Journal of Physics 4.
Journal Article
8 (3), eabk0627 (2022)
First-passage statistics of colloids on fractals: Theory and experimental realization. Science Advances 5.
Journal Article
11 (4), 041047 (2021)
Emergent memory and kinetic hysteresis in strongly driven networks. Physical Review X 6.
Journal Article
269, 108131 (2021)
BetheSF V2: 3-point propagator and additional external potentials. Computer Physics Communications 7.
Journal Article
11 (3), 031067 (2021)
Criticality in cell adhesion. Physical Review X 8.
Journal Article
54 (35), 355601 (2021)
Time- and ensemble-average statistical mechanics of the Gaussian network model. Journal of Physics A 9.
Journal Article
266, 108022 (2021)
Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package. Computer Physics Communications 10.
Journal Article
127 (8), 080601 (2021)
Thermodynamic uncertainty relation bounds the extent of anomalous diffusion. Physical Review Letters 11.
Journal Article
433 (17), 167002 (2021)
The persistent question of potassium channel permeation mechanisms. Journal of Molecular Biology 12.
Journal Article
12, 4466 (2021)
Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Nature Communications 13.
Journal Article
264, 107931 (2021)
GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. Computer Physics Communications 14.
Journal Article
12, 3606 (2021)
Tight docking of membranes before fusion represents a novel, metastable state with unique properties. Nature Communications 15.
Journal Article
3 (2), L022018 (2021)
Toolbox for quantifying memory in dynamics along reaction coordinates. Physical Review Research 16.
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 17.
Journal Article
4, 61 (2021)
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 18.
Journal Article
8 (3), pp. 421 - 430 (2021)
Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ 19.
Journal Article
125 (17), pp. 4241 - 4261 (2021)
Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations. Journal of Physical Chemistry B 20.
Journal Article
49 (7), pp. 4186 - 4195 (2021)
Choice of fluorophore affects dynamic DNA nanostructures. Nucleic Acids Research 21.
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 22.
Journal Article
Per|Mut: Spatially resolved hydration entropies from atomistic simulations. Journal of Chemical Theory and Computation, In Press (2021)
23.
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 24.
Journal Article
50 (2), pp. 181 - 186 (2021)
Lipid–protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal 25.
Journal Article
50 (2), pp. 107 - 108 (2021)
Special issue: Multicomponent lipid membranes—how molecular organisation leads to function. European Biophysics Journal 26.
Journal Article
50 (2), pp. 159 - 172 (2021)
Structure, gating and interactions of the voltage-dependent anion channel. European Biophysics Journal 27.
Journal Article
50 (2), pp. 279 - 293 (2021)
How proteins open fusion pores: insights from molecular simulations. European Biophysics Journal 28.
Journal Article
590 (7846), pp. 509 - 514 (2021)
Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 29.
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 30.
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 31.
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 32.
Journal Article
119 (12), pp. 2418 - 2430 (2020)
Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations. Biophysical Journal 33.
Journal Article
Atomistic simulations of the human proteasome inhibited by a covalent ligand. arXiv, 2012.03387 (2020)
34.
Journal Article
2 (4), 043084 (2020)
Spectral theory of fluctuations in time-average statistical mechanics of reversible and driven systems. Physical Review Research 35.
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 36.
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 37.
Journal Article
16 (11), p. 1237-1245 (2020)
Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine. Nature Chemical Biology 38.
Journal Article
102 (4), 043312 (2020)
Variationally derived intermediates for correlated free-energy estimates between intermediate states. Physical Review E 39.
Journal Article
125 (11), 110602 (2020)
Faster uphill relaxation in thermodynamically equidistant temperature quenches. Physical Review Letters 40.
Journal Article
9, e57589 (2020)
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 41.
Journal Article
16 (9), e1008132 (2020)
Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Computational Biology 42.
Journal Article
7 (5), pp. 835 - 843 (2020)
The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ 43.
Journal Article
49 (6), pp. 497 - 510 (2020)
How accurate is circular dichroism-based model validation? European Biophysics Journal 44.
Journal Article
117 (35), pp. 21014 - 21021 (2020)
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 45.
Journal Article
6 (30), eaba3916 (2020)
Proteasomal degradation of the intrinsically disordered protein tau at single-residue resolution. Science Advances 46.
Journal Article
16 (6), pp. 3504 - 3512 (2020)
Determining free-energy differences through variationally derived intermediates. Journal of Chemical Theory and Computation 47.
Journal Article
17, 13 (2020)
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 48.
Journal Article
11, 2162 (2020)
Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nature Communications 49.
Journal Article
34 (5), pp. 601 - 633 (2020)
The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design 50.
Journal Article
16 (4), pp. 2561 - 2569 (2020)
Probing the accuracy of explicit solvent constant pH molecular dynamics simulations for peptides. Journal of Chemical Theory and Computation 51.
Journal Article
124 (6), pp. 1115 - 1123 (2020)
Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes". The Journal of Physical Chemistry B 52.
Journal Article
28 (2), pp. 215 - 222 (2020)
Structural basis for glycerol efflux and selectivity of human Aquaporin 7. Structure 53.
Journal Article
11 (4), pp. 1140 - 1152 (2020)
Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science 54.
Journal Article
118 (1), pp. 151 - 161 (2020)
tRNA dissociation from EF-Tu after GTP hydrolysis: Primary steps and antibiotic inhibition. Biophysical Journal 55.
Journal Article
16 (1), pp. 108 - 118 (2020)
Computing spatially resolved rotational hydration entropies from atomistic simulations. Journal of Chemical Theory and Computation 56.
Journal Article
74 (1), pp. 27 - 43 (2020)
Enhancing NMR derived ensembles with kinetics on multiple timescales. Journal of Biomolecular NMR 57.
Journal Article
5 (12), eaax8030 (2019)
Active role of elongation factor G in maintaining the mRNA reading frame during translation. Science Advances 58.
Journal Article
33, pp. 1031 - 1043 (2019)
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design 59.
Journal Article
10, 5366 (2019)
Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications 60.
Journal Article
7, 182 (2019)
Manifestations of projection-induced memory: General theory and the tilted single file. Frontiers in Physics 61.
Journal Article
40 (27), pp. 2418 - 2431 (2019)
More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 62.
Journal Article
10, 4598 (2019)
Thermodynamic control of −1 programmed ribosomal frameshifting. Nature Communications 63.
Journal Article
15 (9), pp. 5087 - 5102 (2019)
SESCA: Predicting circular dichroism spectra from protein molecular structures. Journal of Chemical Theory and Computation 64.
Journal Article
5 (8), pp. 1468 - 1474 (2019)
Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 65.
Journal Article
5 (7), eaaw6756 (2019)
The conduction pathway of potassium channels is water free under physiological conditions. Science Advances 66.
Journal Article
8, e44718 (2019)
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 67.
Journal Article
52, 244001 (2019)
Extreme value statistics of ergodic Markov processes from first passage times in the large deviation limit. Journal of Physics A: Mathematical and Theoretical 68.
Journal Article
40 (6), pp. 816 - 827 (2019)
Pyruvate carboxylase deficiency type A and type C: Characterization of 5 novel pathogenic variants in PC and analysis of the genotype-phenotype correlation. Human Mutation 69.
Journal Article
116 (9), pp. 1658 - 1666 (2019)
Lipid bilayer composition influences the activity of the antimicrobial peptide dermcidin channel. Biophysical Journal 70.
Journal Article
116 (14), pp. 6594 - 6601 (2019)
Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 71.
Journal Article
8, e43542 (2019)
Automated cryo-EM structure refinement using correlation-driven molecular dynamics. eLife 72.
Journal Article
2019, 024002 (2019)
Interlacing relaxation and first-passage phenomena in reversible discrete and continuous space Markovian dynamics. Journal of Statistical Mechanics: Theory and Experiment 73.
Journal Article
10 (1), 925 (2019)
A molecular mechanism for transthyretin amyloidogenesis. Nature Communications 74.
Journal Article
363 (6429), pp. 875 - 880 (2019)
A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels. Science 75.
Journal Article
5 (2), pp. 780 - 794 (2019)
Molecular mechanism of polycation-induced pore formation in biomembranes. ACS Biomaterials Science and Engineering 76.
Journal Article
116 (3), pp. 1059 - 1064 (2019)
Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels. Proceedings of the National Academy of Sciences of the United States of America 77.
Journal Article
116 (1), pp. 4 - 11 (2019)
GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal 78.
Journal Article
15 (1), pp. 698 - 707 (2019)
Interpretation of interfacial protein spectra with enhanced molecular simulation ensembles. Journal of Chemical Theory and Computation 79.
Journal Article
59 (10), pp. 4093 - 4099 (2019)
Sharing data from molecular simulations. Journal of Chemical Information and Modeling 80.
Journal Article
15 (3), pp. 2064 - 2070 (2019)
Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation 81.
Journal Article
150 (16), 164120 (2019)
Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics 82.
Journal Article
141 (2), pp. 858 - 869 (2019)
Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society 83.
Journal Article
4 (12), pp. 1708 - 1718 (2018)
Accurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 84.
Journal Article
20 (11), 112002 (2018)
Duality between relaxation and first passage in reversible Markov dynamics: Rugged energy landscapes disentangled. New Journal of Physics 85.
Journal Article
20, 113021 (2018)
Unfolding tagged particle histories in single-file diffusion: Exact single- and two-tag local times beyond large deviation theory. New Journal of Physics 86.
Journal Article
19 (19), pp. 2507 - 2511 (2018)
Transient secondary and tertiary structure formation kinetics in the intrinsically disordered state of α-Synuclein from atomistic simulations. ChemPhysChem 87.
Journal Article
122 (39), pp. 7924 - 7930 (2018)
Quantifying asymmetry of multimeric proteins. The Journal of Physical Chemistry A 88.
Journal Article
51 (34), 343001 (2018)
The 2018 biomembrane curvature and remodeling roadmap. Journal of Physics D: Applied Physics 89.
Journal Article
10 (8), pp. 813 - 820 (2018)
Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chemistry 90.
Journal Article
14 (7), pp. 3397 - 3408 (2018)
Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. Journal of Chemical Theory and Computation 91.
Journal Article
9, 2375 (2018)
Structure determination from single molecule X-ray scattering with three photons per image. Nature Communications 92.
Journal Article
14 (6), pp. 2843 - 2851 (2018)
Kinetics of huperzine A dissociation from acetylcholinesterase via multiple unbinding pathways. Journal of Chemical Theory and Computation 93.
Journal Article
8, 6886 (2018)
In silico assessment of the conduction mechanism of the ryanodine receptor 1 reveals previously unknown exit pathways. Scientific Reports 94.
Journal Article
7, e34353 (2018)
Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit. eLife 95.
Journal Article
49, pp. 27 - 35 (2018)
Molecular simulations of the ribosome and associated translation factors. Current Opinion in Structural Biology 96.
Journal Article
138-139, pp. 85 - 92 (2018)
Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 97.
Journal Article
114 (6), pp. 1336 - 1343 (2018)
Mechanism of mechanosensitive gating of the TREK-2 potassium channel. Biophysical Journal 98.
Journal Article
9, 717 (2018)
A single NaK channel conformation is not enough for non-selective ion conduction. Nature Communications 99.
Journal Article
8 (12), pp. 2791 - 2808 (2017)
Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chemical Neuroscience