Publications
Journal Article (175)
1.
Journal Article
Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews: Computational Molecular Science 13 (1), e1622 (2023)
2.
Journal Article
Chemical Space Exploration with Active Learning and Alchemical Free Energies. Journal of Chemical Theory and Computation 18 (10), pp. 6259 - 6270 (2022)
3.
Journal Article
The clinical drug candidate anle138b binds in a cavity of lipidic α-synuclein fibrils. Nature Communications 13, pp. 5385 - 5394 (2022)
4.
Journal Article
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. Journal of Chemical Infomation and Modeling 62 (7), pp. 1691 - 1711 (2022)
5.
Journal Article
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)
6.
Journal Article
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)
7.
Journal Article
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)
8.
Journal Article
The persistent question of potassium channel permeation mechanisms. Journal of Molecular Biology 433 (17), 167002 (2021)
9.
Journal Article
Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 4, 61 (2021)
10.
Journal Article
Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ 8 (3), pp. 421 - 430 (2021)
11.
Journal Article
Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations. Journal of Physical Chemistry B 125 (17), pp. 4241 - 4261 (2021)
12.
Journal Article
One plus one makes three: Triangular coupling of correlated amino acid mutations. Journal of Physical Chemistry Letters 12 (12), pp. 3195 - 3201 (2021)
13.
Journal Article
ATP-magnesium coordination: Protein structure-based force field evaluation and corrections. Journal of Chemical Theory and Computation 17 (3), pp. 1922 - 1930 (2021)
14.
Journal Article
Lipid–protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal 50 (2), pp. 181 - 186 (2021)
15.
Journal Article
Special issue: Multicomponent lipid membranes—how molecular organisation leads to function. European Biophysics Journal 50 (2), pp. 107 - 108 (2021)
16.
Journal Article
Structure, gating and interactions of the voltage-dependent anion channel. European Biophysics Journal 50 (2), pp. 159 - 172 (2021)
17.
Journal Article
Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 590 (7846), pp. 509 - 514 (2021)
18.
Journal Article
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)
19.
Journal Article
Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine. Nature Chemical Biology 16 (11), p. 1237-1245 (2020)
20.
Journal Article
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 9, e57589 (2020)
21.
Journal Article
The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ 7 (5), pp. 835 - 843 (2020)
22.
Journal Article
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)
23.
Journal Article
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 17, 13 (2020)
24.
Journal Article
Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nature Communications 11, 2162 (2020)
25.
Journal Article
The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design 34 (5), pp. 601 - 633 (2020)
26.
Journal Article
Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes". The Journal of Physical Chemistry B 124 (6), pp. 1115 - 1123 (2020)
27.
Journal Article
Structural basis for glycerol efflux and selectivity of human Aquaporin 7. Structure 28 (2), pp. 215 - 222 (2020)
28.
Journal Article
Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science 11 (4), pp. 1140 - 1152 (2020)
29.
Journal Article
Enhancing NMR derived ensembles with kinetics on multiple timescales. Journal of Biomolecular NMR 74 (1), pp. 27 - 43 (2020)
30.
Journal Article
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design 33, pp. 1031 - 1043 (2019)
31.
Journal Article
Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications 10, 5366 (2019)
32.
Journal Article
More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 40 (27), pp. 2418 - 2431 (2019)
33.
Journal Article
Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 5 (8), pp. 1468 - 1474 (2019)
34.
Journal Article
The conduction pathway of potassium channels is water free under physiological conditions. Science Advances 5 (7), eaaw6756 (2019)
35.
Journal Article
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8, e44718 (2019)
36.
Journal Article
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 40 (6), pp. 816 - 827 (2019)
37.
Journal Article
Lipid bilayer composition influences the activity of the antimicrobial peptide dermcidin channel. Biophysical Journal 116 (9), pp. 1658 - 1666 (2019)
38.
Journal Article
A molecular mechanism for transthyretin amyloidogenesis. Nature Communications 10 (1), 925 (2019)
39.
Journal Article
A pharmacological master key mechanism that unlocks the selectivity filter gate in K+ channels. Science 363 (6429), pp. 875 - 880 (2019)
40.
Journal Article
Molecular mechanism of polycation-induced pore formation in biomembranes. ACS Biomaterials Science and Engineering 5 (2), pp. 780 - 794 (2019)
41.
Journal Article
Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels. Proceedings of the National Academy of Sciences of the United States of America 116 (3), pp. 1059 - 1064 (2019)
42.
Journal Article
GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal 116 (1), pp. 4 - 11 (2019)
43.
Journal Article
Interpretation of interfacial protein spectra with enhanced molecular simulation ensembles. Journal of Chemical Theory and Computation 15 (1), pp. 698 - 707 (2019)
44.
Journal Article
Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation 15 (3), pp. 2064 - 2070 (2019)
45.
Journal Article
Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics 150 (16), 164120 (2019)
46.
Journal Article
Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society 141 (2), pp. 858 - 869 (2019)
47.
Journal Article
Accurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 4 (12), pp. 1708 - 1718 (2018)
48.
Journal Article
Quantifying asymmetry of multimeric proteins. The Journal of Physical Chemistry A 122 (39), pp. 7924 - 7930 (2018)
49.
Journal Article
Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nature Chemistry 10 (8), pp. 813 - 820 (2018)
50.
Journal Article
Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. Journal of Chemical Theory and Computation 14 (7), pp. 3397 - 3408 (2018)
51.
Journal Article
In silico assessment of the conduction mechanism of the ryanodine receptor 1 reveals previously unknown exit pathways. Scientific Reports 8, 6886 (2018)
52.
Journal Article
Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 138-139, pp. 85 - 92 (2018)
53.
Journal Article
Mechanism of mechanosensitive gating of the TREK-2 potassium channel. Biophysical Journal 114 (6), pp. 1336 - 1343 (2018)
54.
Journal Article
A single NaK channel conformation is not enough for non-selective ion conduction. Nature Communications 9, 717 (2018)
55.
Journal Article
Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chemical Neuroscience 8 (12), pp. 2791 - 2808 (2017)
56.
Journal Article
Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes. Journal of Chemical Theory and Computation 13 (12), pp. 6275 - 6289 (2017)
57.
Journal Article
Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy. Archives of Biochemistry and Biophysics 628, pp. 81 - 91 (2017)
58.
Journal Article
Temperature dependence of protein-water interactions in a gated yeast aquaporin. Scientific Reports 7, 4016 (2017)
59.
Journal Article
Gating charge calculations by computational electrophysiology simulations. Biophysical Journal 112 (7), pp. 1396 - 1405 (2017)
60.
Journal Article
Role of pore-lining residues in defining the rate of water conduction by Aquaporin-0. Biophysical Journal 112 (5), pp. 953 - 965 (2017)
61.
Journal Article
Localization and ordering of lipids around Aquaporin-0: Proteinand lipid mobility effects. Frontiers in Physiology 8, 124 (2017)
62.
Journal Article
pmx Webserver: A user friendly interface for alchemistry. Journal of Chemical Information and Modeling 57 (2), pp. 109 - 114 (2017)
63.
Journal Article
CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods 14 (1), pp. 71 - 73 (2017)
64.
Journal Article
Voltage dependence of conformational dynamics and subconducting states of VDAC-1. Biophysical Journal 111 (6), pp. 1223 - 1234 (2016)
65.
Journal Article
Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proceedings of the National Academy of Sciences of the United States of America 113 (37), pp. 10358 - 10363 (2016)
66.
Journal Article
An atomistic view of amyloidogenic self-assembly: Structure and dynamics of heterogeneous conformational states in the pre-nucleation phase. Scientific Reports 6, 33156 (2016)
67.
Journal Article
Aquaporin 4 as a NH3 channel. Journal of Biological Chemistry 291 (36), pp. 19184 - 19195 (2016)
68.
Journal Article
Insights into the function of ion channels by computational electrophysiology simulations. Biochimica et Biophysica Acta - Biomembranes 1858 (7, B), pp. 1741 - 1752 (2016)
69.
Journal Article
Accurate and rigorous prediction of the changes in protein free energies in a large-scale mutation scan. Angewandte Chemie-International Edition 55 (26), pp. 7364 - 7368 (2016)
70.
Journal Article
Partial least squares for dependent data. Biometrika 103 (2), pp. 351 - 362 (2016)
71.
Journal Article
Crystal structure of an ammonia-permeable aquaporin. PLOS Biology 14 (3), e1002411 (2016)
72.
Journal Article
Allosteric switch regulates protein–protein binding through collective motion. Proceedings of the National Academy of Sciences of the United States of America 113 (12), pp. 3269 - 3274 (2016)
73.
Journal Article
A non-canonical voltage sensor controls gating in K2P K2 channels. Cell 164 (5), pp. 937 - 949 (2016)
74.
Journal Article
H95 is a pH-dependent gate in Aquaporin 4. Structure 23 (12), pp. 2309 - 2318 (2015)
75.
Journal Article
Role of structural dynamics at the receptor G protein interface for signal transduction. PLOS One 10 (11), e0143399 (2015)
76.
Journal Article
Structural ensembles of intrinsically disordered proteins depend strongly on force field: A comparison to experiment. Journal of Chemical Theory and Computation 11 (11), pp. 5513 - 5524 (2015)
77.
Journal Article
Improved validation of IDP ensembles by one-bond Cα-Hα scalar couplings. Journal of Biomolecular NMR 63 (3), pp. 299 - 307 (2015)
78.
Journal Article
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry 36 (26), pp. 1990 - 2008 (2015)
79.
Journal Article
The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility. Proceedings of the National Academy of Sciences of the United States of America 112 (40), pp. 12390 - 12395 (2015)
80.
Journal Article
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. arXiv, 1507.00898v1 (2015)
81.
Journal Article
ClC-K chloride channels: Emerging pathophysiology of Bartter syndrome type 3. American Journal of Physiology-Renal Physiology 308 (12), pp. F1324 - F1334 (2015)
82.
Journal Article
Binding affinities controlled by shifting conformational equilibria: Opportunities and limitations. Biophysical Journal 108 (10), pp. 2585 - 2590 (2015)
83.
Journal Article
Pmx: Automated protein structure and topology generation for alchemical perturbations. Journal of Computational Chemistry 36 (5), pp. 348 - 354 (2015)
84.
Journal Article
Mechanisms of anion conduction by coupled glutamate transporters. Cell 160 (3), pp. 542 - 553 (2015)
85.
Journal Article
Population shuffling of protein conformations. Angewandte Chemie International Edition 54 (1), pp. 207 - 210 (2015)
86.
Journal Article
Ion permeation in K+ channels occurs by direct Coulomb knock-on. Science 345 (6207), pp. 352 - 355 (2014)
87.
Journal Article
A designed conformational shift to control protein binding specificity. Angewandte Chemie International Edition 53 (39), pp. 10367 - 10371 (2014)
88.
Journal Article
Spontaneous aggregation of the insulin-derived steric zipper peptide VEALYL results in different aggregation forms with common features. Journal of Molecular Biology 426 (2), pp. 362 - 376 (2014)
89.
Journal Article
Quantifying artifacts in Ewald simulations of inhomogeneous systems with a net charge. Journal of Chemical Theory and Computation 10 (1), pp. 381 - 390 (2014)
90.
Journal Article
Phosphorylation drives a dynamic switch in serine/arginine-rich proteins. Structure 21 (12), pp. 2162 - 2174 (2013)
91.
Journal Article
Computational analysis of local membrane properties. Journal of Computer-Aided Molecular Design 27 (10), pp. 845 - 858 (2013)
92.
Journal Article
How the dynamics of the metal-binding loop region controls the acid transition in cupredoxins. Biochemistry 52 (42), pp. 7397 - 7404 (2013)
93.
Journal Article
Collective dynamics underlying allosteric transitions in hemoglobin. PLoS Computational Biology 9 (9), e1003232 (2013)
94.
Journal Article
Phosphorylation of rat aquaporin-4 at Ser111 is not required for channel gating. Glia 61 (7), pp. 1101 - 1112 (2013)
95.
Journal Article
Probing the energy landscape of activation gating of the bacterial potassium channel KcsA. PLoS Computational Biology 9 (5), e1003058 (2013)
96.
Journal Article
The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site. Molecular Membrane Biology 30 (3), pp. 246 - 260 (2013)
97.
Journal Article
Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proceedings of the National Academy of Sciences of the United States of America 110 (12), pp. 4586 - 4591 (2013)
98.
Journal Article
Discovery of novel human aquaporin-1 blockers. ACS Chemical Biology 8 (1), pp. 249 - 256 (2013)
99.
Journal Article
Optimal superpositioning of flexible molecule ensemble. Biophysical Journal 104 (1), pp. 196 - 207 (2013)