Prof. Dr. Bert L. de Groot

Name Card

Main Affiliation

Max-Planck-Institut für Biophysikalische Chemie

Staff Status

campusgoe

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2023 | Preprint
Bayesian Maximum Entropy Ensemble Refinement
Eltzner, B.; Hofstadler, J.; Rudolf, D.; Habeck, M.& de Groot, B. (2023). DOI: https://doi.org/10.1101/2023.09.12.557310
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2022 | Zeitschriftenartikel
Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR
Öster, C.; Tekwani Movellan, K.; Goold, B.; Hendriks, K.; Lange, S.; Becker, S. & de Groot, B. L. u.a. (2022)
Journal of the American Chemical Society, 144(9) pp. 4147-4157. DOI: https://doi.org/10.1021/jacs.1c13247
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2022 | Zeitschriftenartikel
Pre-Exascale Computing of Protein–Ligand Binding Free Energies with Open Source Software for Drug Design
Gapsys, V.; Hahn, D. F.; Tresadern, G.; Mobley, D. L.; Rampp, M. & de Groot, B. L. (2022)
Journal of Chemical Information and Modeling, 62(5) pp. 1172-1177. DOI: https://doi.org/10.1021/acs.jcim.1c01445
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2022 | Preprint
The 3D structure of lipidic fibrils of α-synuclein
Frieg, B.; Antonschmidt, L.; Dienemann, C.; Geraets, J. A.; Najbauer, E. E.; Matthes, D.& de Groot, B. L. u.a. (2022). DOI: https://doi.org/10.1101/2022.03.02.481946
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2022 | Zeitschriftenartikel
GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design
Kutzner, C.; Kniep, C.; Cherian, A.; Nordstrom, L.; Grubmüller, H. ; de Groot, B. L. & Gapsys, V. (2022)
Journal of Chemical Information and Modeling, art. acs.jcim.2c00044. DOI: https://doi.org/10.1021/acs.jcim.2c00044
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2022 | Zeitschriftenartikel | Research Paper
Pre‐exascale HPC approaches for molecular dynamics simulations. Covid‐19 research: A use case
Wieczór, M.; Genna, V.; Aranda, J.; Badia, R. M.; Gelpí, J. L.; Gapsys, V. & de Groot, B. L. u.a. (2022)
Wiley Interdisciplinary Reviews. Computational Molecular Science,. DOI: https://doi.org/10.1002/wcms.1622
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2022 | Zeitschriftenartikel |
A litmus test for classifying recognition mechanisms of transiently binding proteins
Chakrabarti, K. S.; Olsson, S.; Pratihar, S. ; Giller, K. ; Overkamp, K.; Lee, K. O. & Gapsys, V. u.a. (2022)
Nature Communications, 13(1). DOI: https://doi.org/10.1038/s41467-022-31374-5
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2022 | Zeitschriftenartikel |
Chemical Space Exploration with Active Learning and Alchemical Free Energies
Khalak, Y.; Tresadern, G.; Hahn, D. F.; de Groot, B. L. & Gapsys, V. (2022)
Journal of Chemical Theory and Computation, art. acs.jctc.2c00752. DOI: https://doi.org/10.1021/acs.jctc.2c00752
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2022 | Zeitschriftenartikel |
The 3D structure of lipidic fibrils of α-synuclein
Frieg, B.; Antonschmidt, L.; Dienemann, C.; Geraets, J. A.; Najbauer, E. E.; Matthes, D. & de Groot, B. L. u.a. (2022)
Nature Communications, 13(1). DOI: https://doi.org/10.1038/s41467-022-34552-7
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2021 | Zeitschriftenartikel
The Persistent Question of Potassium Channel Permeation Mechanisms
Mironenko, A.; Zachariae, U.; de Groot, B. L. & Kopec, W. (2021)
Journal of Molecular Biology, 433(17) art. S0022283621002035. DOI: https://doi.org/10.1016/j.jmb.2021.167002
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2021 | Zeitschriftenartikel
One Plus One Makes Three: Triangular Coupling of Correlated Amino Acid Mutations
Werner, M.; Gapsys, V. & de Groot, B. L. (2021)
The Journal of Physical Chemistry Letters, 12(12) pp. 3195-3201. DOI: https://doi.org/10.1021/acs.jpclett.1c00380
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2021 | Zeitschriftenartikel
Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations
Baumann, H. M.; Gapsys, V.; de Groot, B. L. & Mobley, D. L. (2021)
The Journal of Physical Chemistry B, 125(17) pp. 4241-4261. DOI: https://doi.org/10.1021/acs.jpcb.0c10263
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2021 | Zeitschriftenartikel
ATP–Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections
Buelens, F. P.; Leonov, H.; de Groot, B. L. & Grubmüller, H. (2021)
Journal of Chemical Theory and Computation, 17(3) pp. 1922-1930. DOI: https://doi.org/10.1021/acs.jctc.0c01205
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2021 | Zeitschriftenartikel
Visualization of the mechanosensitive ion channel MscS under membrane tension
Zhang, Y.; Daday, C.; Gu, R.-X.; Cox, C. D.; Martinac, B.; de Groot, B. L. & Walz, T. (2021)
Nature, 590(7846) pp. 509-514. DOI: https://doi.org/10.1038/s41586-021-03196-w
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2021 | Zeitschriftenartikel
Structural plasticity of the selectivity filter in a nonselective ion channel
Roy, R. N.; Hendriks, K.; Kopec, W.; Abdolvand, S.; Weiss, K. L.; de Groot, B. L. & Lange, A. u.a. (2021)
IUCrJ, 8(3) pp. 421-430. DOI: https://doi.org/10.1107/S205225252100213X
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2021 | Zeitschriftenartikel
Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IXβ Reductase B as a Novel Thrombocytopenia Therapeutic Target
Kim, M.; Ha, J.-H.; Choi, J.; Kim, B.-R.; Gapsys, V.; Lee, K. O. & Jee, J.-G. u.a. (2021)
Journal of Medicinal Chemistry, 65(3) pp. 2548-2557. DOI: https://doi.org/10.1021/acs.jmedchem.1c01664
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2021 | Zeitschriftenartikel |
Special issue: Multicomponent lipid membranes—how molecular organisation leads to function
de Groot, B. L. ; Janshoff, A. ; Steinem, C. & Zweckstetter, M. (2021)
European Biophysics Journal, 50(2) pp. 107-108. DOI: https://doi.org/10.1007/s00249-021-01535-3
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2021 | Zeitschriftenartikel |
Alchemical absolute protein–ligand binding free energies for drug design
Khalak, Y.; Tresadern, G.; Aldeghi, M.; Baumann, H. M.; Mobley, D. L.; de Groot, B. L. & Gapsys, V. (2021)
Chemical Science, 12(41) pp. 13958-13971. DOI: https://doi.org/10.1039/D1SC03472C
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2021 | Zeitschriftenartikel |
Accurate absolute free energies for ligand–protein binding based on non-equilibrium approaches
Gapsys, V.; Yildirim, A.; Aldeghi, M.; Khalak, Y.; van der Spoel, D. & de Groot, B. L. (2021)
Communications Chemistry, 4(1) art. 61. DOI: https://doi.org/10.1038/s42004-021-00498-y
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2020 | Zeitschriftenartikel
Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine
Rabe von Pappenheim, F.; Aldeghi, M.; Shome, B.; Begley, T.; de Groot, B. L. & Tittmann, K. (2020)
Nature Chemical Biology, 16(11) pp. 1237-1245. DOI: https://doi.org/10.1038/s41589-020-0628-4
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2020 | Zeitschriftenartikel
Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes”
Gapsys, V. ; Khabiri, M.; de Groot, B. L. & Freddolino, P. L. (2020)
The Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 124(6) pp. 1115-1123. DOI: https://doi.org/10.1021/acs.jpcb.8b04187
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2020 | Zeitschriftenartikel
A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL
Schubeis, T.; Le Marchand, T.; Daday, C.; Kopec, W.; Tekwani Movellan, K.; Stanek, J. & Schwarzer, T. S. u.a. (2020)
Proceedings of the National Academy of Sciences of the United States of America, 117(35) pp. 21014-21021. DOI: https://doi.org/10.1073/pnas.2002598117
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2020 | Zeitschriftenartikel
The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation
Langan, P. S.; Vandavasi, V. G.; Kopec, W.; Sullivan, B.; Afonne, P. V.; Weiss, K. L. & de Groot, B. L. u.a. (2020)
IUCrJ, 7(5) pp. 835-843. DOI: https://doi.org/10.1107/S2052252520008271
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2020 | Zeitschriftenartikel
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations
Rizzi, A.; Jensen, T.; Slochower, D. R.; Aldeghi, M.; Gapsys, V. ; Ntekoumes, D. & Bosisio, S. u.a. (2020)
Journal of Computer-Aided Molecular Design, 34(5) pp. 601-633. DOI: https://doi.org/10.1007/s10822-020-00290-5
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2020 | Zeitschriftenartikel
Structural Basis for Glycerol Efflux and Selectivity of Human Aquaporin 7
de Maré, S. W.; Venskutonytė, R.; Eltschkner, S.; de Groot, B. L. & Lindkvist-Petersson, K. (2020)
Structure, 28(2) pp. 215-222.e3. DOI: https://doi.org/10.1016/j.str.2019.11.011
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2020 | Zeitschriftenartikel |
Large scale relative protein ligand binding affinities using non-equilibrium alchemy
Gapsys, V. ; Pérez-Benito, L.; Aldeghi, M.; Seeliger, D.; van Vlijmen, H.; Tresadern, G. & de Groot, B. L. (2020)
Chemical Science, 11(4) pp. 1140-1152. DOI: https://doi.org/10.1039/C9SC03754C
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2020 | Zeitschriftenartikel |
On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size
Gapsys, V. & de Groot, B. L. (2020)
eLife, 9. DOI: https://doi.org/10.7554/eLife.57589
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2020 | Zeitschriftenartikel |
Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors
Bastys, T.; Gapsys, V. ; Walter, H.; Heger, E.; Doncheva, N. T.; Kaiser, R. & de Groot, B. L. u.a. (2020)
Retrovirology, 17(1). DOI: https://doi.org/10.1186/s12977-020-00520-6
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2020 | Zeitschriftenartikel |
Lipid-protein interactions modulate the conformational equilibrium of a potassium channel
Gu, R.-X. & de Groot, B. L. (2020)
Nature Communications, 11(1). DOI: https://doi.org/10.1038/s41467-020-15741-8
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2020 | Zeitschriftenartikel |
Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software
Khalak, Y.; Tresadern, G.; de Groot, B. L. & Gapsys, V. (2020)
Journal of Computer-Aided Molecular Design, 35(1) pp. 49-61. DOI: https://doi.org/10.1007/s10822-020-00359-1
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2020 | Zeitschriftenartikel |
Lipid–protein forces predict conformational changes in a mechanosensitive channel
Daday, C. & de Groot, B. L. (2020)
European Biophysics Journal,. DOI: https://doi.org/10.1007/s00249-020-01488-z
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2019 | Zeitschriftenartikel
Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques
Rovó, P.; Smith, C. A. ; Gauto, D.; de Groot, B. L. ; Schanda, P. & Linser, R. (2019)
Journal of the American Chemical Society, 141(2) pp. 858-869. DOI: https://doi.org/10.1021/jacs.8b09258
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2019 | Zeitschriftenartikel
A pharmacological master key mechanism that unlocks the selectivity filter gate in K + channels
Schewe, M.; Sun, H. ; Mert, Ü.; Mackenzie, A.; Pike, A. C. W.; Schulz, F. & Constantin, C. u.a. (2019)
Science, 363(6429) pp. 875-880. DOI: https://doi.org/10.1126/science.aav0569
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2019 | Zeitschriftenartikel
Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric Kv1 channels
Cordeiro, S.; Finol-Urdaneta, R. K.; Köpfer, D.; Markushina, A.; Song, J.; French, R. J. & Kopec, W. u.a. (2019)
Proceedings of the National Academy of Sciences of the United States of America, 116(3) pp. 1059-1064. DOI: https://doi.org/10.1073/pnas.1813161116
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2019 | Zeitschriftenartikel
Gromaps: A Gromacs-Based Toolset to Analyse Density Maps Derived from Molecular Dynamics Simulations
Briones, R. ; Blau, C. ; Kutzner, C.; de Groot, B. L. & Aponte-Santamaría, C. (2019)
Biophysical Journal, 116(3) pp. 142a-143a. DOI: https://doi.org/10.1016/j.bpj.2018.11.790
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2019 | Zeitschriftenartikel
GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations
Briones, R. ; Blau, C. ; Kutzner, C.; de Groot, B. L. & Aponte-Santamaría, C. (2019)
Biophysical Journal, 116(1) pp. 4-11. DOI: https://doi.org/10.1016/j.bpj.2018.11.3126
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2019 | Zeitschriftenartikel
A Pharmacological Masterkey Mechanism to Unlock the Selectivity Filter Gate in K+ Channels
Schewe, M.; Sun, H. ; Mackenzie, A.; Pike, A. C. W.; Schulz, F.; Constantin, C. & Kiper, A. K. u.a. (2019)
Biophysical Journal, 116(3) pp. 301a-302a. DOI: https://doi.org/10.1016/j.bpj.2018.11.1635
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2019 | Zeitschriftenartikel
Thermodynamic Coupling - Free Energy Calculations of Correlated Amino Acid Mutations
Werner, M. & de Groot, B. L. (2019)
Biophysical Journal, 116(3) pp. 463a. DOI: https://doi.org/10.1016/j.bpj.2018.11.2501
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2019 | Zeitschriftenartikel
Molecular Simulations of Ion Permeation, Gating and Selectivity in K+ Channels
Kopec, W. & de Groot, B. L. (2019)
Biophysical Journal, 116(3) pp. 16a. DOI: https://doi.org/10.1016/j.bpj.2018.11.127
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2019 | Zeitschriftenartikel
Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset
Elisée, E.; Gapsys, V. ; Mele, N.; Chaput, L.; Selwa, E.; de Groot, B. L. & Iorga, B. I. (2019)
Journal of Computer-Aided Molecular Design, 33(12) pp. 1031-1043. DOI: https://doi.org/10.1007/s10822-019-00232-w
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2019 | Zeitschriftenartikel
Pyruvate carboxylase deficiency type A and type C: Characterization of five novel pathogenic variants in PC and analysis of the genotype-phenotype correlation
Coci, E. G.; Gapsys, V. ; Shur, N.; Shin‐Podskarbi, Y.; de Groot, B. L. ; Miller, K. & Vockley, J. u.a. (2019)
Human Mutation, 40(6) pp. 816-827. DOI: https://doi.org/10.1002/humu.23742
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2019 | Zeitschriftenartikel
More bang for your buck: Improved use of GPU nodes for GROMACS 2018
Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B. L. & Grubmüller, H. (2019)
Journal of Computational Chemistry, 40(27) pp. 2418-2431. DOI: https://doi.org/10.1002/jcc.26011
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2019 | Zeitschriftenartikel
Predicting Kinase Inhibitor Resistance: Physics-Based and Data-Driven Approaches
Aldeghi, M.; Gapsys, V. & de Groot, B. L. (2019)
ACS Central Science, 5(8) pp. 1468-1474. DOI: https://doi.org/10.1021/acscentsci.9b00590
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2019 | Zeitschriftenartikel
Lipid Bilayer Composition Influences the Activity of the Antimicrobial Peptide Dermcidin Channel
Song, C. ; de Groot, B. L. & Sansom, M. S. P. (2019)
Biophysical Journal, 116(9) pp. 1658-1666. DOI: https://doi.org/10.1016/j.bpj.2019.03.033
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2019 | Zeitschriftenartikel
The conduction pathway of potassium channels is water free under physiological conditions
Öster, C.; Hendriks, K.; Kopec, W.; Chevelkov, V.; Shi, C.; Michl, D. & Lange, S. u.a. (2019)
Science Advances, 5(7) art. eaaw6756. DOI: https://doi.org/10.1126/sciadv.aaw6756
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2019 | Zeitschriftenartikel
Identification of kinetic order parameters for non-equilibrium dynamics
Paul, F.; Wu, H.; Vossel, M.; de Groot, B. L. & Noé, F. (2019)
The Journal of Chemical Physics, 150(16) pp. 164120. DOI: https://doi.org/10.1063/1.5083627
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2019 | Zeitschriftenartikel |
Enhancing NMR derived ensembles with kinetics on multiple timescales
Smith, C. A. ; Mazur, A. ; Rout, A. K.; Becker, S. ; Lee, D. ; de Groot, B. L. & Griesinger, C. (2019)
Journal of Biomolecular NMR, 74(1) pp. 27-43. DOI: https://doi.org/10.1007/s10858-019-00288-8
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2019 | Zeitschriftenartikel |
Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'
Gapsys, V. & de Groot, B. L. (2019)
eLife, 8. DOI: https://doi.org/10.7554/eLife.44718
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2019 | Zeitschriftenartikel |
A molecular mechanism for transthyretin amyloidogenesis
Yee, A. W.; Aldeghi, M.; Blakeley, M. P.; Ostermann, A.; Mas, P. J.; Moulin, M. & de Sanctis, D. u.a. (2019)
Nature Communications, 10(1). DOI: https://doi.org/10.1038/s41467-019-08609-z
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2019 | Zeitschriftenartikel |
Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling
Kopec, W.; Rothberg, B. S. & de Groot, B. L. (2019)
Nature Communications, 10(1). DOI: https://doi.org/10.1038/s41467-019-13227-w
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2018 | Zeitschriftenartikel
In silico assessment of the conduction mechanism of the Ryanodine Receptor 1 reveals previously unknown exit pathways
Heinz, L. P.; Kopec, W.; de Groot, B. L. & Fink, R. H. A. (2018)
Scientific Reports, 8(1). DOI: https://doi.org/10.1038/s41598-018-25061-z
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2018 | Zeitschriftenartikel
Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels
Kopec, W.; Köpfer, D. A.; Vickery, O. N.; Bondarenko, A. S.; Jansen, T. L. C.; de Groot, B. L. & Zachariae, U. (2018)
Nature Chemistry, 10(8) pp. 813-820. DOI: https://doi.org/10.1038/s41557-018-0105-9
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2018 | Zeitschriftenartikel
Quantifying Asymmetry of Multimeric Proteins
Brennecke, J. T. & de Groot, B. L. (2018)
The Journal of Physical Chemistry. A, Molecules, spectroscopy, kinetics, environment & general theory, 122(39) pp. 7924-7930. DOI: https://doi.org/10.1021/acs.jpca.8b06843
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2018 | Zeitschriftenartikel
Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets
Sabo, T. M. ; Gapsys, V. ; Walter, K. F. A.; Fenwick, R. B.; Becker, S. ; Salvatella, X. & de Groot, B. L. u.a. (2018)
Methods, 138-139 pp. 85-92. DOI: https://doi.org/10.1016/j.ymeth.2018.04.007
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2018 | Zeitschriftenartikel
Accurate Estimation of Ligand Binding Affinity Changes upon Protein Mutation
Aldeghi, M.; Gapsys, V. & de Groot, B. L. (2018)
ACS Central Science, 4(12) pp. 1708-1718. DOI: https://doi.org/10.1021/acscentsci.8b00717
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2018 | Zeitschriftenartikel
A Unified Framework for Alchemical Mutations in Proteins, DNA and Ligands
Gapsys, V. & de Groot, B. L. (2018)
Biophysical Journal, 114(3) pp. 674a. DOI: https://doi.org/10.1016/j.bpj.2017.11.3634
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2018 | Zeitschriftenartikel
Mechanism of Mechanosensitive Gating of the TREK-2 Potassium Channel
Brennecke, J. T. & de Groot, B. L. (2018)
Biophysical Journal, 114(6) pp. 1336-1343. DOI: https://doi.org/10.1016/j.bpj.2018.01.030
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2018 | Zeitschriftenartikel
ATP as a Fuel Molecule: Evolutionary Selection of Magnesium-ATP Interaction Mode Facilitates Lossless Chemomechanical Coupling for ATPases
Buelens, F. P.; Leonov, H.; de Groot, B. L. & Grubmüller, H. (2018)
Biophysical Journal, 114(3) pp. 680a. DOI: https://doi.org/10.1016/j.bpj.2017.11.3668
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2018 | Zeitschriftenartikel
Interpretation of Interfacial Protein Spectra with Enhanced Molecular Simulation Ensembles
Lutz, H.; Jaeger, V.; Weidner, T. & de Groot, B. L. (2018)
Journal of Chemical Theory and Computation, 15(1) pp. 698-707. DOI: https://doi.org/10.1021/acs.jctc.8b00840
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2018 | Zeitschriftenartikel
A single NaK channel conformation is not enough for non-selective ion conduction
Shi, C.; He, Y.; Hendriks, K.; de Groot, B. L. ; Cai, X.; Tian, C. & Lange, A. u.a. (2018)
Nature Communications, 9(1). DOI: https://doi.org/10.1038/s41467-018-03179-y
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2018 | Zeitschriftenartikel
Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations
Bastys, T.; Gapsys, V. ; Doncheva, N. T.; Kaiser, R.; de Groot, B. L. & Kalinina, O. V. (2018)
Journal of Chemical Theory and Computation, 14(7) pp. 3397-3408. DOI: https://doi.org/10.1021/acs.jctc.7b01109
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2017 | Zeitschriftenartikel
Temperature dependence of protein-water interactions in a gated yeast aquaporin
Aponte-Santamaría, C.; Fischer, G.; Båth, P.; Neutze, R. & de Groot, B. L. (2017)
Scientific Reports, 7(1). DOI: https://doi.org/10.1038/s41598-017-04180-z
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2017 | Zeitschriftenartikel
pmx Webserver: A User Friendly Interface for Alchemistry
Gapsys, V. & de Groot, B. L. (2017)
Journal of Chemical Information and Modeling, 57(2) pp. 109-114. DOI: https://doi.org/10.1021/acs.jcim.6b00498
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2017 | Zeitschriftenartikel
Role of Pore-Lining Residues in Defining the Rate of Water Conduction by Aquaporin-0
Saboe, P. O.; Rapisarda, C.; Kaptan, S.; Hsiao, Y.-S.; Summers, S. R.; De Zorzi, R. & Dukovski, D. u.a. (2017)
Biophysical Journal, 112(5) pp. 953-965. DOI: https://doi.org/10.1016/j.bpj.2017.01.026
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2017 | Zeitschriftenartikel
Gating Charge Calculations by Computational Electrophysiology Simulations
Machtens, J.-P.; Briones, R. ; Alleva, C.; de Groot, B. L. & Fahlke, C. (2017)
Biophysical Journal, 112(7) pp. 1396-1405. DOI: https://doi.org/10.1016/j.bpj.2017.02.016
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2017 | Zeitschriftenartikel
CHARMM36: An Improved Force Field for Folded and Intrinsically Disordered Proteins
Huang, J.; Rauscher, S.; Nawrocki, G.; Ran, T.; Feig, M.; de Groot, B. L. & Grubmüller, H. u.a. (2017)
Biophysical Journal, 112(3) pp. 175a-176a. DOI: https://doi.org/10.1016/j.bpj.2016.11.971
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2017 | Zeitschriftenartikel
Molecular Simulations of Ion Permeation in Potassium Channels
Kopec, W. & de Groot, B. (2017)
Biophysical Journal, 112(3) pp. 163a. DOI: https://doi.org/10.1016/j.bpj.2016.11.898
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2017 | Zeitschriftenartikel
Alchemical Free Energy Calculations for Nucleotide Mutations in Protein–DNA Complexes
Gapsys, V. & de Groot, B. L. (2017)
Journal of Chemical Theory and Computation, 13(12) pp. 6275-6289. DOI: https://doi.org/10.1021/acs.jctc.7b00849
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2017 | Zeitschriftenartikel
Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects
Briones, R. ; Aponte-Santamaría, C. & de Groot, B. L. (2017)
Frontiers in Physiology, 8. DOI: https://doi.org/10.3389/fphys.2017.00124
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2017 | Zeitschriftenartikel
Ions in Action - Studying Ion Channels by Computational Electrophysiology in GROMACS
Kutzner, C.; Ullmann, R. T.; de Groot, B. L. ; Zachariae, U. & Grubmüller, H. (2017)
Biophysical Journal, 112(3) pp. 139a. DOI: https://doi.org/10.1016/j.bpj.2016.11.769
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2017 | Zeitschriftenartikel |
Author Correction: Temperature dependence of protein-water interactions in a gated yeast aquaporin
Aponte-Santamaría, C.; Fischer, G.; Båth, P.; Neutze, R. & de Groot, B. L. (2017)
Scientific Reports, 7(1). DOI: https://doi.org/10.1038/s41598-017-17040-7
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2017 | Zeitschriftenartikel
Resolving the Atomistic Modes of Anle138b Inhibitory Action on Peptide Oligomer Formation
Matthes, D. ; Gapsys, V. ; Griesinger, C. & de Groot, B. L. (2017)
ASC Chemical Neuroscience, 8(12) pp. 2791-2808. DOI: https://doi.org/10.1021/acschemneuro.7b00325
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2017 | Zeitschriftenartikel
Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy
Ban, D. ; Smith, C. A. ; de Groot, B. L. ; Griesinger, C. & Lee, D. (2017)
Archives of Biochemistry and Biophysics, 628 pp. 81-91. DOI: https://doi.org/10.1016/j.abb.2017.05.016
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2016 | Zeitschriftenartikel
Allostery through Protein Motion at Different Length and Time Scales
Smith, C. A. ; Mazur, A. ; Ban, D. ; Becker, S. ; Griesinger, C. ; Lee, D. & de Groot, B. L. (2016)
Biophysical Journal, 110(3, Supplement 1) pp. 221a. DOI: https://doi.org/10.1016/j.bpj.2015.11.1226
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2016 | Zeitschriftenartikel
Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC
Ilgü, H.; Jeckelmann, J.-M.; Gapsys, V. ; Ucurum, Z.; de Groot, B. L. & Fotiadis, D. (2016)
Proceedings of the National Academy of Sciences of the United States of America, 113(37) pp. 10358-10363. DOI: https://doi.org/10.1073/pnas.1605442113
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2016 | Zeitschriftenartikel
Aquaporin 4 as a NH3 Channel
Assentoft, M.; Kaptan, S.; Schneider, H.-P.; Deitmer, J. W.; de Groot, B. L. & MacAulay, N. (2016)
The Journal of Biological Chemistry, 291(36) pp. 19184-19195. DOI: https://doi.org/10.1074/jbc.M116.740217
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2016 | Zeitschriftenartikel
Accurate and Rigorous Prediction of the Changes in Protein Free Energies in a Large-Scale Mutation Scan
Gapsys, V. ; Michielssens, S.; Seeliger, D. & de Groot, B. L. (2016)
Angewandte Chemie. International Edition, 55(26) pp. 7364-7368. DOI: https://doi.org/10.1002/anie.201510054
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2016 | Zeitschriftenartikel | Research Paper
Partial least squares for dependent data
Singer, M. ; Krivobokova, T. ; Munk, A. & Groot, B. L. de (2016)
Biometrika, 103(2) pp. 351-362. DOI: https://doi.org/10.1093/biomet/asw010
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2016 | Zeitschriftenartikel
Crystal Structure of an Ammonia-Permeable Aquaporin
Kirscht, A.; Kaptan, S. S.; Bienert, G. P.; Chaumont, F.; Nissen, P.; de Groot, B. L. & Kjellbom, P. u.a. (2016)
PLOS Biology, 14(3) pp. e1002411. DOI: https://doi.org/10.1371/journal.pbio.1002411
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2016 | Zeitschriftenartikel
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
Rauscher, S.; Gapsys, V. ; Zhou, M.; Van, Q. ; Gajda, M.; Zweckstetter, M. & Enderlein, J. u.a. (2016)
Biophysical Journal, 110(3) pp. 358a. DOI: https://doi.org/10.1016/j.bpj.2015.11.1932
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2016 | Konferenzbeitrag (Abstract)
The Molecular Dynamics of Ion Channel Permeation, Selectivity and Gating
de Groot, B. L. ; Koepfer, D.; Song, C. ; Gruene, T.; Sheldrick, G. M. & Zachariae, U. (2016)
Biophysical Journal, 110(3) p. 9a. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA.
Cambridge: Cell Press. DOI: https://doi.org/10.1016/j.bpj.2015.11.101
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2016 | Zeitschriftenartikel
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, J.; Rauscher, S.; Nawrocki, G.; Ran, T.; Feig, M.; Groot, B. L. de & Grubmüller, H. u.a. (2016)
Nature Methods, 14(1) pp. 71-73. DOI: https://doi.org/10.1038/nmeth.4067
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2016 | Zeitschriftenartikel
A Non-canonical Voltage-Sensing Mechanism Controls Gating in K2P K+ Channels
Schewe, M.; Nematian-Ardestani, E.; Sun, H. ; Musinszki, M.; Cordeiro, S.; Bucci, G. & de Groot, B. L. u.a. (2016)
Cell, 164(5) pp. 937-949. DOI: https://doi.org/10.1016/j.cell.2016.02.002
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2016 | Zeitschriftenartikel
Gating Charge Calculations: Probing Voltage-Sensing Proteins through Computational Electrophysiology
Machtens, J.-P.; Briones, R. ; de Groot, B. L. & Fahlke, C. (2016)
Biophysical Journal, 110(3) pp. 106a. DOI: https://doi.org/10.1016/j.bpj.2015.11.628
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2016 | Zeitschriftenartikel
A Non-Canonical Voltage Sensor Controls Gating in K2P K+ Channels
Schewe, M.; Nematian-Ardestani, E.; Sun, H. ; Musinszki, M.; Cordeiro, S.; Bucci, G. & de Groot, B. L. u.a. (2016)
Biophysical Journal, 110(3) pp. 277a. DOI: https://doi.org/10.1016/j.bpj.2015.11.1502
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2016 | Zeitschriftenartikel
Global and Local Conformational Heterogeniety Governs the Pre-Nucleation Phase in Amyloidogenic Self-Assembly
Matthes, D. ; Gapsys, V. ; Brennecke, J. T. & de Groot, B. L. (2016)
Biophysical Journal, 110(3) pp. 402a. DOI: https://doi.org/10.1016/j.bpj.2015.11.2170
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2016 | Zeitschriftenartikel
Insights from the First Principles Based Large Scale Protein Thermostability Calculations
Gapsys, V. ; Michielssens, S.; Seeliger, D. & de Groot, B. L. (2016)
Biophysical Journal, 110(3) pp. 368a. DOI: https://doi.org/10.1016/j.bpj.2015.11.1985
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2016 | Zeitschriftenartikel
Insights into the function of ion channels by computational electrophysiology simulations
Kutzner, C.; Köpfer, D. A.; Machtens, J.-P.; de Groot, B. L. ; Song, C. & Zachariae, U. (2016)
Biochimica et Biophysica Acta. Biomembranes, 1858(7) pp. 1741-1752. DOI: https://doi.org/10.1016/j.bbamem.2016.02.006
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2016 | Zeitschriftenartikel |
An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase
Matthes, D. ; Gapsys, V. ; Brennecke, J. T. & de Groot, B. L. (2016)
Scientific Reports, 6(1). DOI: https://doi.org/10.1038/srep33156
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2016 | Zeitschriftenartikel | Research Paper |
Voltage Dependence of Conformational Dynamics and Subconducting States of VDAC-1
Briones, R. ; Weichbrodt, C. ; Paltrinieri, L.; Mey, I. ; Villinger, S. ; Giller, K. & Lange, A. u.a. (2016)
Biophysical Journal, 111(6) pp. 1223-1234. DOI: https://doi.org/10.1016/j.bpj.2016.08.007
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2016 | Zeitschriftenartikel | Research Paper
Allosteric switch regulates protein-protein binding through collective motion
Smith, C. A. ; Ban, D. ; Pratihar, S. ; Giller, K. ; Paulat, M. ; Becker, S. & Griesinger, C. u.a. (2016)
Proceedings of the National Academy of Sciences, 113(12) pp. 3269-3274. DOI: https://doi.org/10.1073/pnas.1519609113
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2015 | Zeitschriftenartikel
Xen crystallography - choose your radiation
Gruene, T.; Hahn, H. W.; Luebben, A. V.; Meilleur, F.; Sheldrick, G. M. ; Köpfer, D. A. & Song, C. u.a. (2015)
Acta Crystallographica. Section A, Foundations and Advances, 71(a1) pp. s44-s44. DOI: https://doi.org/10.1107/S2053273315099301
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2015 | Zeitschriftenartikel
The membrane anchor of the transcriptional activator SREBP is characterized by intrinsic conformational flexibility
Linser, R. ; Salvi, N.; Briones, R. ; Rovó, P.; de Groot, B. L. & Wagner, G. (2015)
Proceedings of the National Academy of Sciences of the United States of America, 112(40) pp. 12390-12395. DOI: https://doi.org/10.1073/pnas.1513782112
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2015 | Zeitschriftenartikel
Ion Permeation in Potassium Channels Involves Direct Coulomb Knock-On between Ions
Zachariae, U.; Kopfer, D. A.; Song, C. ; Gruene, T.; Sheldrick, G. M. & de Groot, B. L. (2015)
Biophysical Journal, 108(2) pp. 118a. DOI: https://doi.org/10.1016/j.bpj.2014.11.663
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2015 | Zeitschriftenartikel
His 95 Acts as a pH Gate in Aquaporin-4
Kaptan, S. S. & de Groot, B. L. (2015)
Biophysical Journal, 108(2) pp. 316a. DOI: https://doi.org/10.1016/j.bpj.2014.11.1718
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2015 | Zeitschriftenartikel
Conformational Dynamics and Functional Asymmetry of ABCE1, a Ribosome Recycling Protein
Leonov, H.; de Groot, B. L. & Grubmüller, H. (2015)
Biophysical Journal, 108(2) pp. 512a. DOI: https://doi.org/10.1016/j.bpj.2014.11.2806
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2015 | Zeitschriftenartikel
Microsecond Motion Modulates Ubiquitin Binding through an Allosteric Backbone/Side Chain Network
Smith, C. A. ; Ban, D. ; Giller, K. ; Becker, S. ; Griesinger, C. ; Lee, D. & Groot, B. L. de (2015)
Biophysical Journal, 108(2) pp. 184a-185a. DOI: https://doi.org/10.1016/j.bpj.2014.11.1020
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2015 | Zeitschriftenartikel
H95 Is a pH-Dependent Gate in Aquaporin 4
Kaptan, S.; Assentoft, M.; Schneider, H. P.; Fenton, R. A.; Deitmer, J. W.; MacAulay, N. & de Groot, B. L. (2015)
Structure, 23(12) pp. 2309-2318. DOI: https://doi.org/10.1016/j.str.2015.08.020
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2015 | Zeitschriftenartikel
Mechanisms of Anion Conduction by Coupled Glutamate Transporters
Machtens, J.-P.; Kortzak, D.; Lansche, C.; Leinenweber, A.; Kilian, P.; Begemann, B. & Zachariae, U. u.a. (2015)
Cell, 160(3) pp. 542-553. DOI: https://doi.org/10.1016/j.cell.2014.12.035
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2015 | Zeitschriftenartikel
Structural Ensembles of Intrinsically Disordered Proteins using Molecular Dynamics Simulation
Rauscher, S.; Gapsys, V. ; de Groot, B. L. & Grubmüller, H. (2015)
Biophysical Journal, 108(2) pp. 14a. DOI: https://doi.org/10.1016/j.bpj.2014.11.100
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2015 | Zeitschriftenartikel
Direct Contacts of K+ Ions in the Selectivity Filter Enable the High Conductance of K+ Channels
Song, C. ; Gruene, T.; Sheldrick, G. M. ; Sansom, M. S. P.; Zachariae, U.; de Groot, B. L. & Köpfer, D. A. (2015)
Biophysical Journal, 108(2) pp. 129a. DOI: https://doi.org/10.1016/j.bpj.2014.11.721
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2015 | Zeitschriftenartikel |
Corruption and inequality of wealth amongst the very rich
Franses, P. H. & de Groot, B. (2015)
Quality & Quantity, 50(3) pp. 1245-1252. DOI: https://doi.org/10.1007/s11135-015-0202-4
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2015 | Zeitschriftenartikel | Research Paper
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
Kutzner, C.; Pall, S.; Fechner, M.; Esztermann, A.; Groot, B. L. de & Grubmüller, H. (2015)
Journal of Computational Chemistry, 36(26) pp. 1990-2008. DOI: https://doi.org/10.1002/jcc.24030
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2015 | Zeitschriftenartikel | Research Paper
Binding Affinities Controlled by Shifting Conformational Equilibria: Opportunities and Limitations
Michielssens, S.; Groot, B. L. de & Grubmüller, H. (2015)
Biophysical Journal, 108(10) pp. 2585-2590. DOI: https://doi.org/10.1016/j.bpj.2015.04.012
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2015 | Zeitschriftenartikel | Research Paper
Population Shuffling of Protein Conformations
Smith, C. A. ; Ban, D. ; Pratihar, S. ; Giller, K. ; Schwiegk, C. ; Groot, B. L. de & Becker, S. u.a. (2015)
Angewandte Chemie International Edition, 54(1) pp. 207-210. DOI: https://doi.org/10.1002/anie.201408890
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2015 | Zeitschriftenartikel | Research Paper
Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment
Rauscher, S.; Gapsys, V. ; Gajda, M. J.; Zweckstetter, M. ; Groot, B. L. de & Grubmüller, H. (2015)
Journal of Chemical Theory and Computation, 11(11) pp. 5513-5524. DOI: https://doi.org/10.1021/acs.jctc.5b00736
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2015 | Zeitschriftenartikel
Improved validation of IDP ensembles by one-bond C alpha-H alpha scalar couplings
Gapsys, V. ; Narayanan, R. L.; Xiang, S.; de Groot, B. L. & Zweckstetter, M. (2015)
Journal of Biomolecular NMR, 63(3) pp. 299-307. DOI: https://doi.org/10.1007/s10858-015-9990-z
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2014 | Zeitschriftenartikel
Ion Permeation Efficiency through Potassium Channels
Kopfer, D. A.; Song, C. ; Zachariae, U. & de Groot, B. L. (2014)
Biophysical Journal, 106(2) pp. 539a. DOI: https://doi.org/10.1016/j.bpj.2013.11.3005
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2014 | Zeitschriftenartikel
Controlling Protein Binding Specificity by a Conformational Shift
Michielssens, S.; Peters, J. H.; Ban, D. ; Pratihar, S. ; Becker, S. ; Sabo, T. M. & Giller, K. u.a. (2014)
Biophysical Journal, 106(2) pp. 439a. DOI: https://doi.org/10.1016/j.bpj.2013.11.2471
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2014 | Zeitschriftenartikel
Membrane-Dependent Activity of the Dermcidin Channel
Song, C. ; de Groot, B. L. & Sansom, M. S. P. (2014)
Biophysical Journal, 106(2) pp. 297a. DOI: https://doi.org/10.1016/j.bpj.2013.11.1728
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2014 | Zeitschriftenartikel
Anion Permeation through Excitatory Amino Acid Transporters
Machtens, J.-P.; Lansche, C.; Leinenweber, A.; Kilian, P.; Begemann, B.; Zachariae, U. & Ewers, D. u.a. (2014)
Biophysical Journal, 106(2) pp. 149a. DOI: https://doi.org/10.1016/j.bpj.2013.11.858
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2014 | Zeitschriftenartikel
pmx: Automated protein structure and topology generation for alchemical perturbations
Gapsys, V.; Michielssens, S.; Seeliger, D. & de Groot, B. L. (2014)
Journal of Computational Chemistry, 36(5) pp. 348-354. DOI: https://doi.org/10.1002/jcc.23804
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2014 | Zeitschriftenartikel
Ion permeation in K+ channels occurs by direct Coulomb knock-on
Koepfer, D. A.; Song, C. ; Gruene, T.; Sheldrick, G. M. ; Zachariae, U. & de Groot, B. L. (2014)
Science, 346(6207) pp. 352-355. DOI: https://doi.org/10.1126/science.1254840
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2014 | Zeitschriftenartikel | Research Paper
A Designed Conformational Shift To Control Protein Binding Specificity
Michielssens, S.; Peters, J. H.; Ban, D. ; Pratihar, S. ; Seeliger, D.; Sharma, M. & Giller, K. u.a. (2014)
Angewandte Chemie International Edition, 53(39) pp. 10367-10371. DOI: https://doi.org/10.1002/anie.201403102
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2014 | Zeitschriftenartikel | Research Paper
Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge
Hub, J. S. ; Groot, B. L. de ; Grubmüller, H. & Groenhof, G. (2014)
Journal of Chemical Theory and Computation, 10(1) pp. 381-390. DOI: https://doi.org/10.1021/ct400626b
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2014 | Zeitschriftenartikel |
Spontaneous Aggregation of the Insulin-Derived Steric Zipper Peptide VEALYL Results in Different Aggregation Forms with Common Features
Matthes, D. ; Daebel, V.; Meyenberg, K.; Riedel, D. ; Heim, G. ; Diederichsen, U. & Lange, A. u.a. (2014)
Journal of Molecular Biology, 426(2) pp. 362-376. DOI: https://doi.org/10.1016/j.jmb.2013.10.020
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2013 | Zeitschriftenartikel
Do commercial real estate prices have predictive content for GDP?
Franses, P. H. & De Groot, B. (2013)
Applied Economics, 45(31) pp. 4379-4384. DOI: https://doi.org/10.1080/00036846.2013.783681
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2013 | Zeitschriftenartikel
Molecular Recognition through Concerted Ubiquitin Backbone and Side Chain Motion Determined from NMR and MD Simulations
Smith, C. A. ; Ban, D. ; Peters, J. H.; Giller, K. ; Becker, S. ; Groot, B. L. de & Griesinger, C. u.a. (2013)
Biophysical Journal, 104(2) art. 30a. DOI: https://doi.org/10.1016/j.bpj.2012.11.203
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2013 | Zeitschriftenartikel
Optimal Superpositioning of Flexible Molecule Ensembles
Gapsys, V. & de Groot, B. L. (2013)
Biophysical Journal, 104(1) pp. 196-207. DOI: https://doi.org/10.1016/j.bpj.2012.11.003
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2013 | Zeitschriftenartikel
Phosphorylation of rat aquaporin-4 at Ser 111 is not required for channel gating
Assentoft, M.; Kaptan, S.; Fenton, R. A.; Hua, S. Z.; de Groot, B. L. & MacAulay, N. (2013)
Glia, 61(7) pp. 1101-1112. DOI: https://doi.org/10.1002/glia.22498
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2013 | Zeitschriftenartikel
The identification of novel, high affinity AQP9 inhibitors in an intracellular binding site
Wacker, S. J.; Aponte-Santamaría, C.; Kjellbom, P.; Nielsen, S.; de Groot, B. L. & Rützler, M. (2013)
Molecular Membrane Biology, 30(3) pp. 246-260. DOI: https://doi.org/10.3109/09687688.2013.773095
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2013 | Zeitschriftenartikel
Collective Dynamics Underlying Allosteric Transitions in Hemoglobin
Vesper, M. D. & de Groot, B. L. (2013)
PLoS Computational Biology, 9(9) pp. e1003232. DOI: https://doi.org/10.1371/journal.pcbi.1003232
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2013 | Zeitschriftenartikel
Discovery of Novel Human Aquaporin-1 Blockers
Seeliger, D.; Zapater, C.; Krenc, D.; Haddoub, R.; Flitsch, S.; Beitz, E. & Cerdà, J. u.a. (2013)
ACS Chemical Biology, 8(1) pp. 249-256. DOI: https://doi.org/10.1021/cb300153z
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2013 | Konferenzbeitrag (Abstract)
Channel Crystal Structure and Antimicrobial Mechanism of Dermcidin from Human Skin
Song, C. ; Weichbrodt, C. ; Dynowski, M.; Steinem, C. ; Zachariae, U.; Zeth, K. & de Groot, B. L. u.a. (2013)
Biophysical Journal, 104(2) p. 241a. , Philadelphia, PA.
Cambridge: Cell Press. DOI: https://doi.org/10.1016/j.bpj.2012.11.1359
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2013 | Zeitschriftenartikel
How the Dynamics of the Metal-Binding Loop Region Controls the Acid Transition in Cupredoxins
Paltrinieri, L.; Borsari, M.; Battistuzzi, G.; Sola, M.; Dennison, C.; de Groot, B. L. & Corni, S. u.a. (2013)
Biochemistry (Washington), 52(42) pp. 7397-7404. DOI: https://doi.org/10.1021/bi400860n
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2013 | Zeitschriftenartikel
Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA
Linder, T.; de Groot, B. L. & Stary-Weinzinger, A. (2013)
PLoS Computational Biology, 9(5) pp. e1003058. DOI: https://doi.org/10.1371/journal.pcbi.1003058
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2013 | Zeitschriftenartikel |
Computational analysis of local membrane properties
Gapsys, V. ; de Groot, B. L. & Briones, R. (2013)
Journal of Computer-Aided Molecular Design, 27(10) pp. 845-858. DOI: https://doi.org/10.1007/s10822-013-9684-0
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2013 | Zeitschriftenartikel | Research Paper
Crystal structure and functional mechanism of a human antimicrobial membrane channel
Song, C. ; Weichbrodt, C. ; Salnikov, E. S.; Dynowski, M.; Forsberg, B. O. ; Bechinger, B. & Steinem, C. u.a. (2013)
Proceedings of the National Academy of Sciences, 110(12) pp. 4586-4591. DOI: https://doi.org/10.1073/pnas.1214739110
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2013 | Zeitschriftenartikel | Research Paper
Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins
Xiang, S.; Gapsys, V. ; Kim, H.-Y.; Bessonov, S.; Hsiao, H.-H.; Moehlmann, S. & Klaukien, V. u.a. (2013)
Structure, 21(12) pp. 2162-2174. DOI: https://doi.org/10.1016/j.str.2013.09.014
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2012 | Zeitschriftenartikel
Identification of selective inhibitors of the potassium channel Kv1.1-1.2((3)) by high-throughput virtual screening and automated patch clamp
Wacker, S. J.; Jurkowski, W.; Simmons, K.; Fishwick, C.; Johnson, A. P.; Madge, D. & Lindahl, E. u.a. (2012)
ChemMedChem, 7(10) pp. 1775-1783. DOI: https://doi.org/10.1002/cmdc.201100600
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2012 | Zeitschriftenartikel
Molecular Dynamics in Principal Component Space
Michielssens, S.; van Erp, T. S.; Kutzner, C.; Ceulemans, A. & de Groot, B. L. (2012)
The Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 116(29) pp. 8350-8354. DOI: https://doi.org/10.1021/jp209964a
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2012 | Zeitschriftenartikel
Specificity Profiles for DNA-Binding Proteins from Exhaustive In-Silico Screening
Seeliger, D.; Buelens, F. P.; Goette, M.; de Groot, B. L. & Grubmüller, H. (2012)
Biophysical Journal, 102(3) pp. 73a. DOI: https://doi.org/10.1016/j.bpj.2011.11.429
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2012 | Zeitschriftenartikel
Computational Electrophysiology Reveals Ion Channel Permeation in Atomistic Detail
Zachariae, U.; Kutzner, C.; Grubmüller, H. & de Groot, B. L. (2012)
Biophysical Journal, 102(3) pp. 22a. DOI: https://doi.org/10.1016/j.bpj.2011.11.147
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2012 | Zeitschriftenartikel
Molecular Determinants in K+ Channel hERG Inactivation Gating
Kopfer, D. A.; Hahn, U.; Ohmert, I.; Vriend, G.; Pongs, O.; de Groot, B. L. & Zachariae, U. (2012)
Biophysical Journal, 102(3) pp. 529a-530a. DOI: https://doi.org/10.1016/j.bpj.2011.11.2894
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2012 | Zeitschriftenartikel
Structure and Dynamics of the Human Antimicrobial Peptide Dermcidin Oligomer: It is an Ion Channel
Song, C. ; Bordignon, E.; Dynowski, M.; Markov, G.; de Groot, B. L. ; Zachariae, U. & Zeth, K. (2012)
Biophysical Journal, 102(3) pp. 471a. DOI: https://doi.org/10.1016/j.bpj.2011.11.2584
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2012 | Zeitschriftenartikel
Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations
Matthes, D. ; Gapsys, V. & de Groot, B. L. (2012)
Journal of Molecular Biology, 421(2-3) pp. 390-416. DOI: https://doi.org/10.1016/j.jmb.2012.02.004
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2012 | Zeitschriftenartikel
Common socio-economic cycle periods
de Groot, B. & Franses, P. H. (2012)
Technological Forecasting and Social Change, 79(1) pp. 59-68. DOI: https://doi.org/10.1016/j.techfore.2011.06.006
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2012 | Zeitschriftenartikel
Ubiquitin Dynamics in Complexes Reveal Molecular Recognition Mechanisms Beyond Induced Fit and Conformational Selection
Peters, J. H. & de Groot, B. L. (2012)
PLoS Computational Biology, 8(10) pp. e1002704. DOI: https://doi.org/10.1371/journal.pcbi.1002704
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2012 | Zeitschriftenartikel
A Molecular Switch Driving Inactivation in the Cardiac K+ Channel hERG
Köpfer, D. A.; Hahn, U.; Ohmert, I.; Vriend, G.; Pongs, O.; de Groot, B. L. & Zachariae, U. (2012)
PLoS One, 7(7) pp. e41023. DOI: https://doi.org/10.1371/journal.pone.0041023
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2012 | Zeitschriftenartikel
Molecular driving forces defining lipid positions around aquaporin-0
Aponte-Santamaria, C.; Briones, R. ; Schenk, A. D.; Walz, T. & de Groot, B. L. (2012)
Proceedings of the National Academy of Sciences of the United States of America, 109(25) pp. 9887-9892. DOI: https://doi.org/10.1073/pnas.1121054109
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2012 | Zeitschriftenartikel
Exploring the Mechanism and Functional (A)Symmetry of ATP Binding Cassette Domains
Leonov, H.; Vesper, M. & de Groot, B. L. (2012)
Biophysical Journal, 102(3) pp. 452a. DOI: https://doi.org/10.1016/j.bpj.2011.11.2479
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2012 | Zeitschriftenartikel
Ubiquitin Dynamics in Complexes
Peters, J. H. & de Groot, B. L. (2012)
Biophysical Journal, 102(3) pp. 260a. DOI: https://doi.org/10.1016/j.bpj.2011.11.1434
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2012 | Zeitschriftenartikel
Non-Equilibrium Free Energy Calculations for Ligand Optimization
Gapsys, V. ; Seeliger, D. & de Groot, B. L. (2012)
Biophysical Journal, 102(3) pp. 40a. DOI: https://doi.org/10.1016/j.bpj.2011.11.249
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2012 | Zeitschriftenartikel
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations
Gapsys, V. ; Seeliger, D. & de Groot, B. L. (2012)
Journal of Chemical Theory and Computation, 8(7) pp. 2373-2382. DOI: https://doi.org/10.1021/ct300220p
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2012 | Zeitschriftenartikel
Design of Peptide-Membrane Interactions to Modulate Single-File Water Transport through Modified Gramicidin Channels
Portella, G.; Polupanow, T.; Zocher, F.; Boytsov, D. A.; Pohl, P.; Diederichsen, U. & de Groot, B. L. (2012)
Biophysical Journal, 103(8) pp. 1698-1705. DOI: https://doi.org/10.1016/j.bpj.2012.08.059
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2012 | Zeitschriftenartikel | Research Paper |
Partial Least-Squares Functional Mode Analysis: Application to the Membrane Proteins AQP1, Aqy1, and CLC-ec1
Krivobokova, T. ; Briones, R. ; Hub, J. S. ; Munk, A. & Groot, B. L. de (2012)
Biophysical Journal, 103(4) pp. 786-796. DOI: https://doi.org/10.1016/j.bpj.2012.07.022
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2012 | Zeitschriftenartikel | Research Paper
beta-Barrel Mobility Underlies Closure of the Voltage-Dependent Anion Channel
Zachariae, U.; Schneider, R. ; Briones, R. ; Gattin, Z. ; Demers, J.-P.; Giller, K. & Maier, E. u.a. (2012)
Structure, 20(9) pp. 1540-1549. DOI: https://doi.org/10.1016/j.str.2012.06.015
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2011 | Zeitschriftenartikel
Computational electrophysiology: the molecular dynamics of ion channel permeation and selectivity in atomistic detail
Kutzner, C.; Grubmüller, H. ; de Groot, B. L. & Zachariae, U. (2011)
Biophysical Journal, 101(4) pp. 809-817. DOI: https://doi.org/10.1016/j.bpj.2011.06.010
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2011 | Zeitschriftenartikel
Aquaporin-9 Protein Is the Primary Route of Hepatocyte Glycerol Uptake for Glycerol Gluconeogenesis in Mice
Jelen, S.; Wacker, S.; Aponte-Santamaría, C.; Skott, M.; Rojek, A.; Johanson, U. & Kjellbom, P. u.a. (2011)
The Journal of Biological Chemistry, 286(52) pp. 44319-44325. DOI: https://doi.org/10.1074/jbc.M111.297002
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2011 | Zeitschriftenartikel
Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization
Matthes, D. ; Gapsys, V. ; Daebel, V. & de Groot, B. L. (2011)
PLoS One, 6(5) pp. e19129. DOI: https://doi.org/10.1371/journal.pone.0019129
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2011 | Zeitschriftenartikel
Comment on “Molecular Selectivity in Aquaporin Channels Studied by the 3D-RISM Theory”
Hub, J. S. & de Groot, B. L. (2011)
The Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, 115(25) pp. 8364-8366. DOI: https://doi.org/10.1021/jp2022242
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2011 | Zeitschriftenartikel
Computer Simulations of Structure–Activity Relationships for hERG Channel Blockers
Boukharta, L.; Keränen, H.; Stary-Weinzinger, A.; Wallin, G.; de Groot, B. L. & Åqvist, J. (2011)
Biochemistry (Washington), 50(27) pp. 6146-6156. DOI: https://doi.org/10.1021/bi200173n
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2011 | Zeitschriftenartikel | Research Paper
Kinetics of Conformational Sampling in Ubiquitin
Ban, D. ; Funk, M.; Gulich, R.; Egger, D.; Sabo, T. M. ; Walter, K. F. A. & Fenwick, R. B. u.a. (2011)
Angewandte Chemie International Edition, 50(48) pp. 11437-11440. DOI: https://doi.org/10.1002/anie.201105086
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2011 | Zeitschriftenartikel | Research Paper
Towards computional specificity screening of DNA-binding proteins
Seeliger, D.; Buelens, F. P.; Goette, M.; Groot, B. L. de & Grubmüller, H. (2011)
Nucleic Acids Research, 39(19) pp. 8281-8290. DOI: https://doi.org/10.1093/nar/gkr531
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2010 | Zeitschriftenartikel
Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin
Aponte-Santamaría, C.; Hub, J. S. & de Groot, B. L. (2010)
Physical Chemistry, Chemical Physics, 12(35) pp. 10246. DOI: https://doi.org/10.1039/c004384m
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2010 | Zeitschriftenartikel
Potentials of Mean Force and Permeabilities for Carbon Dioxide, Ammonia, and Water Flux across a Rhesus Protein Channel and Lipid Membranes
Hub, J. S. ; Winkler, F. K.; Merrick, M. & de Groot, B. L. (2010)
Journal of the American Chemical Society, 132(38) pp. 13251-13263. DOI: https://doi.org/10.1021/ja102133x
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2010 | Zeitschriftenartikel
The thermodynamic influence of trapped water molecules on a protein-ligand interaction
Stegmann, C. M.; Seeliger, D.; Sheldrick, G. M. ; de Groot, B. L. & Wahl, M. C. (2010)
Acta Crystallographica. Section A, Foundations and Advances, 66(a1) pp. s19-s19. DOI: https://doi.org/10.1107/S0108767310099599
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2010 | Zeitschriftenartikel
Protein Thermostability Calculations Using Alchemical Free Energy Simulations
Seeliger, D. & de Groot, B. L. (2010)
Biophysical Journal, 98(10) pp. 2309-2316. DOI: https://doi.org/10.1016/j.bpj.2010.01.051
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2010 | Zeitschriftenartikel
Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data
Lange, O. F.; van der Spoel, D. & de Groot, B. L. (2010)
Biophysical Journal, 99(2) pp. 647-655. DOI: https://doi.org/10.1016/j.bpj.2010.04.062
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2010 | Zeitschriftenartikel
Detection of Functional Modes in Protein Dynamics
Hub, J. S. ; Van der Spoel, D. & de Groot, B. L. (2010)
Biophysical Journal, 98(3) pp. 566a. DOI: https://doi.org/10.1016/j.bpj.2009.12.3071
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2010 | Zeitschriftenartikel
62 Early Diagnosis of Postoperative Complications After Liver Transplants in Children
Wildeboer, G. J.; Geerts, H. R.; de Groot, B. L. & Ponne, E. D. (2010)
Pediatric Research, 68 pp. 34-35. DOI: https://doi.org/10.1203/00006450-201011001-00062
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2010 | Zeitschriftenartikel
Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation
Hub, J. S. ; Kubitzki, M. B. & de Groot, B. L. (2010)
PLoS Computational Biology, 6(5) pp. e1000774. DOI: https://doi.org/10.1371/journal.pcbi.1000774
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2010 | Zeitschriftenartikel
Conformational Transitions upon Ligand Binding: Holo-Structure Prediction from Apo Conformations
Seeliger, D. & de Groot, B. L. (2010)
PLoS Computational Biology, 6(1) pp. e1000634. DOI: https://doi.org/10.1371/journal.pcbi.1000634
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2010 | Zeitschriftenartikel
A plate reader-based method for cell water permeability measurement
Fenton, R. A.; Moeller, H. B.; Nielsen, S. ; de Groot, B. L. & Rützler, M. (2010)
American Journal of Physiology. Renal Physiology, 298(1) pp. F224-F230. DOI: https://doi.org/10.1152/ajprenal.00463.2009
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2010 | Zeitschriftenartikel
The anti-protozoal drug pentamidine blocks KIR2.x-mediated inward rectifier current by entering the cytoplasmic pore region of the channel
De Boer, T. P.; Nalos, L.; Stary, A.; Kok, B.; Houtman, M. J. C.; Antoons, G. & Van Veen, T. A. B. u.a. (2010)
British Journal of Pharmacology, 159(7) pp. 1532-1541. DOI: https://doi.org/10.1111/j.1476-5381.2010.00658.x
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2010 | Zeitschriftenartikel
Toward a Consensus Model of the hERG Potassium Channel
Stary, A.; Wacker, S.; Boukharta, L.; Zachariae, U.; Karimi-Nejad, Y.; Åqvist, J. & Vriend, G. u.a. (2010)
ChemMedChem, 5(3) pp. 455-467. DOI: https://doi.org/10.1002/cmdc.200900461
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2010 | Zeitschriftenartikel
Collective Dynamics Underlying Allosteric Transitions
Vesper, M. D. & de Groot, B. L. (2010)
Biophysical Journal, 98(3) pp. 440a. DOI: https://doi.org/10.1016/j.bpj.2009.12.2388
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2010 | Zeitschriftenartikel
Conformational Transitions Upon Ligand Binding: Holo Structure Prediction from Apo Conformations
Seeliger, D. & de Groot, B. L. (2010)
Biophysical Journal, 98(3) pp. 428a. DOI: https://doi.org/10.1016/j.bpj.2009.12.2318
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2010 | Zeitschriftenartikel
Binding of glutamate to the umami receptor
López Cascales, J.; Oliveira Costa, S.; de Groot, B. L. & Walters, D. E. (2010)
Biophysical Chemistry, 152(1-3) pp. 139-144. DOI: https://doi.org/10.1016/j.bpc.2010.09.001
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2010 | Zeitschriftenartikel
g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates
Hub, J. S. ; de Groot, B. L. & van der Spoel, D. (2010)
Journal of Chemical Theory and Computation, 6(12) pp. 3713-3720. DOI: https://doi.org/10.1021/ct100494z
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2010 | Zeitschriftenartikel
Augmentation of Single Channel Water Permeability by Modification of Membrane Anchoring
Zocher, F.; Polupanowa, T.; Portella, G.; de Groot, B. L. ; Diederichsen, U. ; Pohl, P. & Boytsov, D. A. (2010)
Biophysical Journal, 98(3) pp. 279a-280a. DOI: https://doi.org/10.1016/j.bpj.2009.12.1526
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2010 | Zeitschriftenartikel
Conformational Flexibility of the hERG K+ Channel Pore Domain
Weinzinger, A.; Knape, K.; Wacker, S. J.; Boukharta, L. & de Groot, B. L. (2010)
Biophysical Journal, 98(3) pp. 120a. DOI: https://doi.org/10.1016/j.bpj.2009.12.656
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2010 | Zeitschriftenartikel
The Spontaneous Aggregation of Steric Zipper Peptides Studied by Molecular Dynamics Simulations
Matthes, D. & de Groot, B. L. (2010)
Biophysical Journal, 98(3) pp. 650a. DOI: https://doi.org/10.1016/j.bpj.2009.12.3561
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2010 | Zeitschriftenartikel
The Gating Mechanism of Yeast Aquaporin Studied by Molecular Dynamics Simulations
Fischer, G.; Kosinska-Eriksson, U.; Aponte-Santamaria, C.; Palmgren, M.; Geijer, C.; Hedfalk, K. & Hohmann, S. u.a. (2010)
Biophysical Journal, 98(3) pp. 225a. DOI: https://doi.org/10.1016/j.bpj.2009.12.1216
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2010 | Zeitschriftenartikel |
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
Seeliger, D. & de Groot, B. L. (2010)
Journal of Computer-Aided Molecular Design, 24(5) pp. 417-422. DOI: https://doi.org/10.1007/s10822-010-9352-6
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2010 | Zeitschriftenartikel | Research Paper
Voltage-Regulated Water Flux through Aquaporin Channels In Silico
Hub, J. S. ; Aponte-Santamaria, C.; Grubmüller, H. & Groot, B. L. de (2010)
Biophysical Journal, 99(12) pp. L97-L99. DOI: https://doi.org/10.1016/j.bpj.2010.11.003
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2010 | Zeitschriftenartikel | Research Paper
Functional dynamics in the voltage-dependent anion channel
Villinger, S. ; Briones, R. ; Giller, K. ; Zachariae, U.; Lange, A. ; Groot, B. L. de & Griesinger, C. u.a. (2010)
Proceedings of the National Academy of Sciences, 107(52) pp. 22546-22551. DOI: https://doi.org/10.1073/pnas.1012310108
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2009 | Zeitschriftenartikel
Cycles in basic innovations
de Groot, B. & Hans Franses, P. (2009)
Technological Forecasting and Social Change, 76(8) pp. 1021-1025. DOI: https://doi.org/10.1016/j.techfore.2009.03.007
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2009 | Zeitschriftenartikel
tCONCOORD-GUI: Visually supported conformational sampling of bioactive molecules
Seeliger, D. & de Groot, B. L. (2009)
Journal of Computational Chemistry, 30(7) pp. 1160-1166. DOI: https://doi.org/10.1002/jcc.21127
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2009 | Zeitschriftenartikel
Crystal Structure of a Yeast Aquaporin at 1.15 Å Reveals a Novel Gating Mechanism
Fischer, G.; Kosinska-Eriksson, U.; Aponte-Santamaría, C.; Palmgren, M.; Geijer, C.; Hedfalk, K. & Hohmann, S. u.a. (2009)
PLoS Biology, 7(6) pp. e1000130. DOI: https://doi.org/10.1371/journal.pbio.1000130
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2009 | Zeitschriftenartikel
Detection of Functional Modes in Protein Dynamics
Hub, J. S. & de Groot, B. L. (2009)
PLoS Computational Biology, 5(8) pp. e1000480. DOI: https://doi.org/10.1371/journal.pcbi.1000480
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2009 | Zeitschriftenartikel
Domain motions of hyaluronan lyase underlying processive hyaluronan translocation
Joshi, H. V.; Jedrzejas, M. J. & de Groot, B. L. (2009)
Proteins, 76(1) pp. 30-46. DOI: https://doi.org/10.1002/prot.22316
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2009 | Zeitschriftenartikel
Determinants of Water Permeability through Nanoscopic Hydrophilic Channels
Portella, G. & de Groot, B. L. (2009)
Biophysical Journal, 96(3) pp. 925-938. DOI: https://doi.org/10.1016/j.bpj.2008.09.059
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2009 | Zeitschriftenartikel
Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes
Matthes, D. & de Groot, B. L. (2009)
Biophysical Journal, 97(2) pp. 599-608. DOI: https://doi.org/10.1016/j.bpj.2009.04.061
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2009 | Zeitschriftenartikel
Predicting free energy changes using structural ensembles
Benedix, A.; Becker, C. M; de Groot, B. L. ; Caflisch, A. & Böckmann, R. A (2009)
Nature Methods, 6(1) pp. 3-4. DOI: https://doi.org/10.1038/nmeth0109-3
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2009 | Zeitschriftenartikel
Testing for harmonic regressors
Franses, P. H.; De Groot, B. & Legerstee, R. (2009)
Journal of Applied Statistics, 36(3) pp. 339-346. DOI: https://doi.org/10.1080/02664760802454837
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2009 | Zeitschriftenartikel
The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction
Stegmann, C. M.; Seeliger, D.; Sheldrick, G. M. ; de Groot, B. L. & Wahl, M. C. (2009)
Angewandte Chemie International Edition, 48(28) pp. 5207-5210. DOI: https://doi.org/10.1002/anie.200900481
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2008 | Buchbeitrag
Dynamics and Energetics of Permeation Through Aquaporins. What Do We Learn from Molecular Dynamics Simulations?
Hub, J. S. ; Grubmüller, H. & Groot, B. L. de (2008)
In:Beitz, E. (Ed.), Aquaporins pp. 57-76. Heidelberg: Springer Nature. DOI: https://doi.org/10.1007/978-3-540-79885-9_3
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2008 | Zeitschriftenartikel
The Molecular Mechanism of Toxin-Induced Conformational Changes in a Potassium Channel: Relation to C-Type Inactivation
Zachariae, U.; Schneider, R. ; Velisetty, P.; Lange, A. ; Seeliger, D.; Wacker, S. J. & Karimi-Nejad, Y. u.a. (2008)
Structure, 16(5) pp. 747-754. DOI: https://doi.org/10.1016/j.str.2008.01.018
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2008 | Zeitschriftenartikel
Not Only Enthalpy: Large Entropy Contribution to Ion Permeation Barriers in Single-File Channels
Portella, G.; Hub, J. S. ; Vesper, M. D. & de Groot, B. L. (2008)
Biophysical Journal, 95(5) pp. 2275-2282. DOI: https://doi.org/10.1529/biophysj.108.130609
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2008 | Zeitschriftenartikel
Mechanism of selectivity in aquaporins and aquaglyceroporins
Hub, J. S. & de Groot, B. L. (2008)
Proceedings of the National Academy of Sciences of the United States of America, 105(4) pp. 1198-1203. DOI: https://doi.org/10.1073/pnas.0707662104
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2008 | Zeitschriftenartikel
The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: A TEE-REX Molecular Dynamics Study
Kubitzki, M. B. & de Groot, B. L. (2008)
Structure, 16(8) pp. 1175-1182. DOI: https://doi.org/10.1016/j.str.2008.04.013
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2008 | Zeitschriftenartikel
Vacuolar Protein Sorting: Two Different Functional States of the AAA-ATPase Vps4p
Hartmann, C.; Chami, M.; Zachariae, U.; de Groot, B. L. ; Engel, A. & Grütter, M. G. (2008)
Journal of Molecular Biology, 377(2) pp. 352-363. DOI: https://doi.org/10.1016/j.jmb.2008.01.010
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2008 | Zeitschriftenartikel
Stability through cycles
de Groot, B. & Franses, P. H. (2008)
Technological Forecasting and Social Change, 75(3) pp. 301-311. DOI: https://doi.org/10.1016/j.techfore.2007.07.004
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2008 | Zeitschriftenartikel | Research Paper |
Is TEA an inhibitor for human aquaporin-1?
Mueller, E. M.; Hub, J. S. ; Grubmüller, H. & Groot, B. L. de (2008)
Pflügers Archiv European Journal of Physiology, 456(4) pp. 663-669. DOI: https://doi.org/10.1007/s00424-007-0422-0
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2008 | Zeitschriftenartikel | Research Paper
Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution
Lange, O. F.; Lakomek, N.-A. ; Farès, C.; Schroeder, G. F.; Walter, K. F. A.; Becker, S. & Meiler, J. u.a. (2008)
Science, 320(5882) pp. 1471-1475. DOI: https://doi.org/10.1126/science.1157092
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2008 | Zeitschriftenartikel | Research Paper |
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics
Lakomek, N.-A. ; Walter, K. F. A.; Farès, C.; Lange, O. F.; Groot, B. L. de ; Grubmüller, H. & Brueschweiler, R. u.a. (2008)
Journal of Biomolecular NMR, 41(3) pp. 139-155. DOI: https://doi.org/10.1007/s10858-008-9244-4
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2008 | Zeitschriftenartikel | Research Paper
Residual dipolar couplings as a tool to study molecular recognition of ubiquitin
Lakomek, N.-A. ; Lange, O. F.; Walter, K. F. A.; Farès, C.; Egger, D.; Lunkenheimer, P. & Meiler, J. u.a. (2008)
Biochemical Society transactions, 36 pp. 1433-1437. DOI: https://doi.org/10.1042/BST0361433
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2008 | Zeitschriftenartikel | Research Paper
Kinetics, statistics, and energetics of lipid membrane electroporation studied by molecular dynamics simulations
Böckmann, R. A.; Groot, B. L. de ; Kakorin, S.; Neumann, E. & Grubmüller, H. (2008)
Biophysical Journal, 95(4) pp. 1837-1850. DOI: https://doi.org/10.1529/biophysj.108.129437
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2007 | Zeitschriftenartikel | Research Paper
Short-range order and collective dynamics of DMPC bilayers: A comparison between molecular dynamics simulations, X-ray, and neutron scattering experiments
Hub, J. S. ; Salditt, T. ; Rheinstädter, M. C. & Groot, B. L. de (2007)
Biophysical Journal, 93(9) pp. 3156-3168. DOI: https://doi.org/10.1529/biophysj.107.104885
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2007 | Zeitschriftenartikel
Atomic contacts in protein structures. A detailed analysis of atomic radii, packing, and overlaps
Seeliger, D. & de Groot, B. L. (2007)
Proteins, 68(3) pp. 595-601. DOI: https://doi.org/10.1002/prot.21447
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2007 | Zeitschriftenartikel
Geometry-Based Sampling of Conformational Transitions in Proteins
Seeliger, D.; Haas, J. & de Groot, B. L. (2007)
Structure, 15(11) pp. 1482-1492. DOI: https://doi.org/10.1016/j.str.2007.09.017
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2007 | Zeitschriftenartikel
Invariance of Single-File Water Mobility in Gramicidin-like Peptidic Pores as Function of Pore Length
Portella, G.; Pohl, P. & de Groot, B. L. (2007)
Biophysical Journal, 92(11) pp. 3930-3937. DOI: https://doi.org/10.1529/biophysj.106.102921
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2007 | Zeitschriftenartikel
Molecular Dynamics Simulations Using Temperature-Enhanced Essential Dynamics Replica Exchange
Kubitzki, M. B. & de Groot, B. L. (2007)
Biophysical Journal, 92(12) pp. 4262-4270. DOI: https://doi.org/10.1529/biophysj.106.103101
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2007 | Zeitschriftenartikel
Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments
Vermeer, L. S.; de Groot, B. L. ; Réat, V.; Milon, A. & Czaplicki, J. (2007)
European Biophysics Journal, 36(8) pp. 919-931. DOI: https://doi.org/10.1007/s00249-007-0192-9
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2007 | Zeitschriftenartikel | Research Paper
Speeding up parallel GROMACS on high-latency networks
Kutzner, C.; Van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; Groot, B. L. de & Grubmüller, H. (2007)
Journal of Computational Chemistry, 28(12) pp. 2075-2084. DOI: https://doi.org/10.1002/jcc.20703
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2006 | Buchbeitrag
Improved GROMACS Scaling on Ethernet Switched Clusters
Kutzner, C.; Van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; Groot, B. L. de & Grubmüller, H. (2006)
In:Träff, Jesper Larsson; Mohr, Bernd; Worringen, Joachim; Dongarra, Jack (Eds.), Recent Advances in Parallel Virtual Machine and Message Passing Interface pp. 404-405. DOI: https://doi.org/10.1007/11846802_57
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2006 | Zeitschriftenartikel
Mobility of a One-Dimensional Confined File of Water Molecules as a Function of File Length
Saparov, S. M.; Pfeifer, J. R.; Al-Momani, L.; Portella, G.; de Groot, B. L. ; Koert, U. & Pohl, P. (2006)
Physical Review Letters, 96(14). DOI: https://doi.org/10.1103/PhysRevLett.96.148101
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2006 | Zeitschriftenartikel
Molekulare Nanomaschinen unter der Lupe: Proteindynamik-Simulationen
Groot, B. L. de ; Böckmann, R. A. & Grubmüller, H. (2006)
Physik in unserer Zeit, 37(2) pp. 73-79. DOI: https://doi.org/10.1002/piuz.200501098
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2006 | Zeitschriftenartikel
Does CO2 Permeate through Aquaporin-1?
Hub, J. S. & de Groot, B. L. (2006)
Biophysical Journal, 91(3) pp. 842-848. DOI: https://doi.org/10.1529/biophysj.106.081406
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2006 | Zeitschriftenartikel
Alternate Structural Conformations of Streptococcus pneumoniae Hyaluronan Lyase: Insights into Enzyme Flexibility and Underlying Molecular Mechanism of Action
Rigden, D. J.; Littlejohn, J. E.; Joshi, H. V.; de Groot, B. L. & Jedrzejas, M. J. (2006)
Journal of Molecular Biology, 358(4) pp. 1165-1178. DOI: https://doi.org/10.1016/j.jmb.2006.02.066
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2006 | Zeitschriftenartikel | Research Paper
Molecular anatomy of a trafficking organelle
Takamori, S.; Holt, M. ; Stenius, K.; Lemke, E. A.; Gronborg, M.; Riedel, D. & Urlaub, H. u.a. (2006)
Cell, 127(4) pp. 831-846. DOI: https://doi.org/10.1016/j.cell.2006.10.030
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2006 | Zeitschriftenartikel | Research Paper
Ligand-release pathways in the pheromone-binding protein of Bombyx mori
Graeter, F. ; de Groot, B. L. ; Jiang, H. & Grubmüller, H. (2006)
Structure, 14(10) pp. 1567-1576. DOI: https://doi.org/10.1016/j.str.2006.08.012
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2006 | Zeitschriftenartikel | Research Paper
Sequential N- to C-terminal SNARE complex assembly drives priming and fusion of secretory vesicles
Sørensen, J. B.; Wiederhold, K.; Müller, E. M.; Milosevic, I. ; Nagy, G.; de Groot, B. L. & Grubmüller, H. u.a. (2006)
EMBO Journal, 25(5) pp. 955-966. DOI: https://doi.org/10.1038/sj.emboj.7601003
Details DOI PMID PMC WoS

2006 | Zeitschriftenartikel | Research Paper
Quaternary ammonium compounds as water channel blockers - Specificity, potency, and site of action
Detmers, F. J. M.; de Groot, B. L. ; Müller, E. M.; Hinton, A.; Konings, I. B. M.; Sze, M. & Flitsch, S. L. u.a. (2006)
Journal of biological chemistry, 281(20) pp. 14207-14214. DOI: https://doi.org/10.1074/jbc.M513072200
Details DOI PMID PMC WoS

2005 | Zeitschriftenartikel
Alternative Splicing of SNAP-25 Regulates Secretion through Nonconservative Substitutions in the SNARE Domain
Nagy, G.; Milošević, I. ; Fasshauer, D.; Müller, E. M.; de Groot, B. L. ; Lang, T. & Wilson, M. C. u.a. (2005)
Molecular Biology of the Cell, 16(12) pp. 5675-5685. DOI: https://doi.org/10.1091/mbc.e05-07-0595
Details DOI

2005 | Zeitschriftenartikel
The 5Å Structure of Heterologously Expressed Plant Aquaporin SoPIP2;1
Kukulski, W.; Schenk, A.; Johanson, U.; Braun, T.; de Groot, B. L. ; Fotiadis, D. & Kjellbom, P. u.a. (2005)
Journal of Molecular Biology, 350(4) pp. 611-616. DOI: https://doi.org/10.1016/j.jmb.2005.05.001
Details DOI

2005 | Zeitschriftenartikel
The 4.5Å Structure of Human AQP2
Schenk, A. D.; Werten, P. J.; Scheuring, S.; de Groot, B. L. ; Müller, S. A.; Stahlberg, H. & Philippsen, A. u.a. (2005)
Journal of Molecular Biology, 350(2) pp. 278-289. DOI: https://doi.org/10.1016/j.jmb.2005.04.030
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2005 | Zeitschriftenartikel | Research Paper
Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations
Heise, H.; Luca, S.; de Groot, B. L. ; Grubmüller, H. & Baldus, M. (2005)
Biophysical Journal, 89(3) pp. 2113-2120. DOI: https://doi.org/10.1529/biophysj.105.059964
Details DOI PMID PMC WoS

2005 | Rezension
The dynamics and energetics of water permeation and proton exclusion in aquaporins
Groot, B. L. de & Grubmüller, H. (2005)
Current Opinion in Structural Biology, 15(2) pp. 176-183. DOI: https://doi.org/10.1016/j.sbi.2005.02.003
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2005 | Zeitschriftenartikel | Research Paper
Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions
Lange, O. F.; Grubmüller, H. & de Groot, B. L. (2005)
Angewandte Chemie International Edition, 44(22) pp. 3394-3399. DOI: https://doi.org/10.1002/anie.200462957
Details DOI PMID PMC WoS

2004 | Zeitschriftenartikel
Aquaporine: die perfekten Wasserfilter der Zelle
Grubmüller, H. & de Groot, B. L. (2004)
Biospektrum: das Magazin für Biowissenschaften, 10(4) pp. 384-386.
Details

2003 | Zeitschriftenartikel
The structure of the aquaporin-1 water channel: A comparison between cryo-electron microscopy and X-ray crystallography
de Groot, B. L. ; Engel, A. & Grubmüller, H. (2003)
Journal of Molecular Biology, 325(3) pp. 485-493. DOI: https://doi.org/10.1016/S0022-2836(02)01233-0
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2003 | Zeitschriftenartikel | Research Paper
The mechanism of proton exclusion in the aquaporin-1 water channel
de Groot, B. L. ; Frigato, T.; Helms, V. & Grubmüller, H. (2003)
Journal of Molecular Biology, 333(2) pp. 279-293. DOI: https://doi.org/10.1016/j.jmb.2003.08.003
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2002 | Zeitschriftenartikel
Proteine als Filter reinsten Wassers
Grubmüller, H. & de Groot, B. L. (2002)
Max Planck Forschung: das Wissenschaftsmagazin der Max-Planck-Gesellschaft, 1 pp. 8-9.
Details

2002 | Zeitschriftenartikel
Aquaporine - Wasserfilter der Zelle
Grubmüller, H. & de Groot, B. L. (2002)
Bioforum : Forschung, Entwicklung, Service, 6 pp. 387-389.
Details

2002 | Zeitschriftenartikel
Mechanism of Hyaluronan Degradation byStreptococcus pneumoniae Hyaluronate Lyase
Jedrzejas, M. J.; Mello, L. V.; de Groot, B. L. & Li, S. (2002)
The Journal of Biological Chemistry, 277(31) pp. 28287-28297. DOI: https://doi.org/10.1074/jbc.M112009200
Details DOI

2002 | Zeitschriftenartikel
Structure and Flexibility of Streptococcus agalactiaeHyaluronate Lyase Complex with Its Substrate
Mello, L. V.; de Groot, B. L. ; Li, S. & Jedrzejas, M. J. (2002)
The Journal of Biological Chemistry, 277(39) pp. 36678-36688. DOI: https://doi.org/10.1074/jbc.M205140200
Details DOI

2002 | Zeitschriftenartikel
Water Permeation through Gramicidin A: Desformylation and the Double Helix: A Molecular Dynamics Study
de Groot, B. L. ; Tieleman, D. P.; Pohl, P. & Grubmüller, H. (2002)
Biophysical Journal, 82(6) pp. 2934-2942. DOI: https://doi.org/10.1016/S0006-3495(02)75634-8
Details DOI

2002 | Rezension
Progress in the analysis of membrane protein structure and function
Werten, P. J. L.; Remigy, H. W.; Groot, B. L. de ; Fotiadis, D.; Philippsen, A.; Stahlberg, H.& Grubmüller, H. u.a. (2002)
FEBS Letters, 529(1) pp. 65-72. DOI: https://doi.org/10.1016/S0014-5793(02)03290-8
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2002 | Rezension
Structure and function of water channels
Fujiyoshi, Y.; Mitsuoka, K.; de Groot, B. L. ; Philippsen, A.; Grubmüller, H. ; Agre, P.& Engel, A. (2002)
Current Opinion in Structural Biology, 12(4) pp. 509-515. DOI: https://doi.org/10.1016/S0959-440X(02)00355-X
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2001 | Zeitschriftenartikel
A refined structure of human aquaporin-1
de Groot, B. ; Engel, A. & Grubmüller, H. (2001)
FEBS Letters, 504(3) pp. 206-211. DOI: https://doi.org/10.1016/S0014-5793(01)02743-0
Details DOI

2001 | Zeitschriftenartikel | Research Paper
Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds
de Groot, B. L. ; Daura, X.; Mark, A. E. & Grubmüller, H. (2001)
Journal of Molecular Biology, 309(1) pp. 299-313. DOI: https://doi.org/10.1006/jmbi.2001.4655
Details DOI PMID PMC WoS

2001 | Zeitschriftenartikel | Research Paper
Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF
de Groot, B. L. & Grubmüller, H. (2001)
Science, 294(5550) pp. 2353-2357. DOI: https://doi.org/10.1126/science.1062459
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2000 | Zeitschriftenartikel
The 6.9-Å Structure of GlpF: A Basis for Homology Modeling of the Glycerol Channel from Escherichia coli
Stahlberg, H.; Braun, T.; de Groot, B. L. ; Philippsen, A.; Borgnia, M. J.; Agre, P. & Kühlbrandt, W. u.a. (2000)
Journal of Structural Biology, 132(2) pp. 133-141. DOI: https://doi.org/10.1006/jsbi.2000.4317
Details DOI

2000 | Zeitschriftenartikel | Research Paper
Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin
Heymann, J. B.; Pfeiffer, M.; Hildebrandt, V.; Kaback, H. R.; Fotiadis, D.; de Groot, B. L. & Engel, A. u.a. (2000)
Structure, 8(6) pp. 643-653. DOI: https://doi.org/10.1016/S0969-2126(00)00151-9
Details DOI

2000 | Zeitschriftenartikel | Research Paper
The fold of human aquaporin 1
de Groot, B. L. ; Heymann, J. B.; Engel, A.; Mitsuoka, K.; Fujiyoshi, Y. & Grubmüller, H. (2000)
Journal of Molecular Biology, 300(4) pp. 987-994. DOI: https://doi.org/10.1006/jmbi.2000.3913
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2000 | Zeitschriftenartikel | Research Paper
Exocytosis requires asymmetry in the central layer of the SNARE complex
Ossig, R.; Schmitt, H. D.; de Groot, B. L. ; Riedel, D. ; Keränen, S.; Ronne, H. & Grubmüller, H. u.a. (2000)
EMBO Journal, 19(22) pp. 6000-6010. DOI: https://doi.org/10.1093/emboj/19.22.6000
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1999 | Zeitschriftenartikel
Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism 1 1Edited by A. R. Fersht
de Groot, B. L. ; Vriend, G. & Berendsen, H. J. C. (1999)
Journal of Molecular Biology, 286(4) pp. 1241-1249. DOI: https://doi.org/10.1006/jmbi.1998.2568
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1999 | Zeitschriftenartikel
A kinetic model for the internal motions of proteins: Diffusion between multiple harmonic wells
Amadei, A.; de Groot, B. L. ; Ceruso, M.-A.; Paci, M.; Di Nola, A. & Berendsen, H. (1999)
Proteins, 35(3) pp. 283-292. DOI: https://doi.org/10.1002/(SICI)1097-0134(19990515)35:3<283::AID-PROT2>3.0.CO;2-R
Details DOI

1998 | Zeitschriftenartikel
Domain motions in bacteriophage T4 lysozyme: A comparison between molecular dynamics and crystallographic data
de Groot, B. L. ; Hayward, S.; van Aalten, D. M. F; Amadei, A. & Berendsen, H. J. C. (1998)
Proteins, 31(2) pp. 116-127. DOI: https://doi.org/10.1002/(SICI)1097-0134(19980501)31:2<116::AID-PROT2>3.0.CO;2-K
Details DOI

1998 | Zeitschriftenartikel
The dynamic regulation of myocardial oxidative phosphorylation: Analysis of the response time of oxygen consumption
van Beek, J. H. G. M.; Tian, X.; Zuurbier, C.; de Groot, B. L. ; van Echteld, C. J. A.; Eijgelshoven, M. H. J. & Hak, J. B. (1998)
Molecular and Cellular Biochemistry, 184(1/2) pp. 321-344. DOI: https://doi.org/10.1023/A:1006817215408
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1997 | Zeitschriftenartikel
Protein dynamics derived from clusters of crystal structures
van Aalten, D. M.; Conn, D. A.; de Groot, B. L. ; Berendsen, H. J.; Findlay, J. B. & Amadei, A. (1997)
Biophysical Journal, 73(6) pp. 2891-2896. DOI: https://doi.org/10.1016/S0006-3495(97)78317-6
Details DOI

1997 | Zeitschriftenartikel
Prediction of protein conformational freedom from distance constraints
de Groot, B. L. ; van Aalten, D. M. F.; Scheek, R. M.; Amadei, A.; Vriend, G. & Berendsen, H. J. C. (1997)
Proteins, 29(2) pp. 240-251. DOI: https://doi.org/10.1002/(SICI)1097-0134(199710)29:2<240::AID-PROT11>3.0.CO;2-O
Details DOI

1996 | Zeitschriftenartikel
Conformational analysis of retinoids and restriction of their dynamics by retinoid-binding proteins
Aalten, D. M. F. van; de Groot, B. L. ; Berendsen, H. J. C. & Findlay, J. B. C. (1996)
Biochemical Journal, 319(2) pp. 543-550. DOI: https://doi.org/10.1042/bj3190543
Details DOI

1996 | Zeitschriftenartikel
An extended sampling of the configurational space of HPr fromE. coli
de Groot, B. L. ; Amadei, A.; Scheek, R. M.; van Nuland, N. A. J. & Berendsen, H. J. C. (1996)
Proteins, 26(3) pp. 314-322. DOI: https://doi.org/10.1002/(SICI)1097-0134(199611)26:3<314::AID-PROT7>3.0.CO;2-D
Details DOI

1996 | Zeitschriftenartikel
The consistency of large concerted motions in proteins in molecular dynamics simulations
de Groot, B. L. ; van Aalten, D.; Amadei, A. & Berendsen, H. (1996)
Biophysical Journal, 71(4) pp. 1707-1713. DOI: https://doi.org/10.1016/S0006-3495(96)79372-4
Details DOI

1996 | Zeitschriftenartikel
Towards an Exhaustive Sampling of the Configurational Spaces of the Two Forms of the Peptide Hormone Guanylin
de Groot, B. L. ; Amadei, A.; van Aalten, D. M. F. & Berendsen, H. J. C. (1996)
Journal of Biomolecular Structure & Dynamics, 13(5) pp. 741-751. DOI: https://doi.org/10.1080/07391102.1996.10508888
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1996 | Zeitschriftenartikel
An Efficient Method for Sampling the Essential Subspace of Proteins
Amadei, A.; Linssen, A. B. M.; de Groot, B. L. ; van Aalten, D. M. F. & Berendsen, H. J. C. (1996)
Journal of Biomolecular Structure & Dynamics, 13(4) pp. 615-625. DOI: https://doi.org/10.1080/07391102.1996.10508874
Details DOI

1995 | Zeitschriftenartikel
Structure from NMR and molecular dynamics: Distance restraining inhibits motion in the essential subspace
Scheek, R. M.; van Nuland, N. A. J.; de Groot, B. L. & Amadei, A. (1995)
Journal of Biomolecular NMR, 6(1) pp. 106-111. DOI: https://doi.org/10.1007/BF00417496
Details DOI

1983 | Zeitschriftenartikel
High-temperature, high-beta plasma heating by weak turbulence in the TORTUR tokamak
De Kluiver, H.; de Groot, B. L. ; Van Der Meiden, H. J.; Hendriks, F. B.; Kolfschoten, A. W.; Oyevaar, T. & Verschuur, J. W. J. u.a. (1983)
Physics Letters. A, 94(3-4) pp. 156-159. DOI: https://doi.org/10.1016/0375-9601(83)90372-9
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1977 | Zeitschriftenartikel
Plasma confinement and skin currents in a small tokamak with turbulent heating
De Kluiver, H.; Barth, R.; Brocken, H. J. B. M.; Caarls, J. J. L.; de Groot, B. L. ; Kalsbeek, H. W. & Piekaar, H. W. u.a. (1977)
Physics Letters. A, 62(3) pp. 157-160. DOI: https://doi.org/10.1016/0375-9601(77)90010-X
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