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Journal Article (148)

1.
Journal Article
Gapsys, V.; de Groot, B. L.: On the importance of statistics in molecular simulations for thermodynamics, kinetics and simulation box size. eLife 9, e57589 (2020)
2.
Journal Article
Langan, P. S.; Vandavasi, V. G.; Kopec, W.; Sullivan, B.; Afonne, P. V.; Weiss, K. L.; de Groot, B. L.; Coates, L.: The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCrJ 7 (5), pp. 835 - 843 (2020)
3.
Journal Article
Schubeis, T.; Le Marchand, T.; Daday, C.; Kopec, W.; Tekwani Movellan, K.; Stanek, J.; Schwarzer, T. S.; Castiglione, K.; de Groot, B. L.; Pintacuda, G. et al.; Andreas, L. B.: A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences of the United States of America 117 (35), pp. 21014 - 21021 (2020)
4.
Journal Article
Rabe von Pappenheim, F.; Aldeghi, M.; Shome, B.; Begley, T.; de Groot, B. L.; Tittmann, K.: Structural basis for antibiotic action of the B1 antivitamin 2′-methoxy-thiamine. Nature Chemical Biology, In Press (2020)
5.
Journal Article
Bastys, T.; Gapsys, V.; Walter, H.; Heger, E.; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.; Kalinina, O. V.: Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 17, 13 (2020)
6.
Journal Article
Gu, R. X.; de Groot, B. L.: Lipid-protein interactions modulate the conformational equilibrium of a potassium channel. Nature Communications 11, 2162 (2020)
7.
Journal Article
de Maré, S. W.; Venskutonytė, R.; Eltschkner, S.; de Groot, B. L.; Lindkvist-Petersson, K.: Structural basis for glycerol efflux and selectivity of human Aquaporin 7. Structure 28 (2), pp. 215 - 222 (2020)
8.
Journal Article
Gapsys, V.; Khabiri, M.; de Groot, B. L.; Freddolino, P. L.: Comment on "Deficiencies in molecular dynamics simulation-based prediction of protein-DNA binding free energy landscapes". The Journal of Physical Chemistry B 124 (6), pp. 1115 - 1123 (2020)
9.
Journal Article
Rizzi, A.; Jensen, T.; Slochower, D. R.; Aldeghi, M.; Gapsys, V.; Ntekoumes, D.; Bosisio, S.; Papadourakis, M.; Henriksen, N. M.; de Groot, B. L. et al.; Cournia, Z.; Dickson, A.; Michel, J.; Gilson, M. K.; Shirts, M. R.; Mobley, D. L.; Chodera, J. D.: The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design, (in press) (2020)
10.
Journal Article
Gapsys, V.; Perez-Benito, L.; Aldeghi, M.; Seeliger, D.; Van Vlijmen, H.; Tresadern, G.; de Groot, B. L.: Large scale relative protein ligand binding affinities using non-equilibrium alchemy. Chemical Science 11 (4), pp. 1140 - 1152 (2020)
11.
Journal Article
Smith, C. A.; Mazur, A.; Rout, A. K.; Becker, S.; Lee, D.; de Groot, B. L.; Griesinger, C.: Enhancing NMR derived ensembles with kinetics on multiple timescales. Journal of Biomolecular NMR 74, pp. 27 - 43 (2020)
12.
Journal Article
Elisee, E.; Gapsys, V.; Mele, N.; Chaput, L.; Selwa, E.; de Groot, B. L.; Iorga, B. I.: Performance evaluation of molecular docking and free energy calculations protocols using the D3R Grand Challenge 4 dataset. Journal of Computer-Aided Molecular Design 33, pp. 1031 - 1043 (2019)
13.
Journal Article
Kopec, W.; Rothberg, B. S.; de Groot, B. L.: Molecular mechanism of a potassium channel gating through activation gate-selectivity filter coupling. Nature Communications 10, 5366 (2019)
14.
Journal Article
Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B. L.; Grubmüller, H.: More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 40 (27), pp. 2418 - 2431 (2019)
15.
Journal Article
Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Predicting kinase inhibitor resistance: Physics-based and data-driven approaches. ACS Central Science 5 (8), pp. 1468 - 1474 (2019)
16.
Journal Article
Öster, C.; Hendriks, K.; Kopec, W.; Chevelkov, V.; Shi, C.; Michl, D.; Lange, S.; Sun, H.; de Groot, B. L.; Lange, A.: The conduction pathway of potassium channels is water free under physiological conditions. Science Advances 5 (7), eaaw6756 (2019)
17.
Journal Article
Gapsys, V.; de Groot, B. L.: Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'. eLife 8, e44718 (2019)
18.
Journal Article
Coci, E. G.; Gapsys, V.; Shur, N.; Shin‐Podskarbi, Y.; de Groot, B.; Miller, K.; Vockley, J.; Sondheimer, N.; Ganetzky, R.; Freisinger, P.: Pyruvate carboxylase deficiency type A and type C: Characterization of 5 novel pathogenic variants in PC and analysis of the genotype-phenotype correlation. Human Mutation 40 (6), pp. 816 - 827 (2019)
19.
Journal Article
Song, C.; de Groot, B. L.; Sansom, M. S. P.: Lipid bilayer composition influences the activity of the antimicrobial peptide dermcidin channel. Biophysical Journal 116 (9), pp. 1658 - 1666 (2019)
20.
Journal Article
Yee, A. W.; Aldeghi, M.; Blakeley, M. P.; Ostermann, A.; Mas, P. J.; Moulin, M.; de Sanctis, D.; Bowler, M. W.; Mueller-Dieckmann, C.; Mitchell, E. P. et al.; Haertlein, M.; de Groot, B. L.; Boeri Erba, E.; Forsyth, V. T.: A molecular mechanism for transthyretin amyloidogenesis. Nature Communications 10 (1), 925 (2019)
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