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