Publications of B. L. de Groot

de Groot, B. L.; Daura, X.; Mark, A. E.; Grubmueller, H.: Essential dynamics of reversible peptide folding: Memory-free conformational dynamics governed by internal hydrogen bonds. Journal of Molecular Biology 309 (1), pp. 299 - 313 (2001)

de Groot, B. L.; Engel, A.; Grubmueller, H.: A refined structure of human Aquaporin 1. FEBS Letters 504 (3), pp. 206 - 211 (2001)

de Groot, B. L.; Grubmueller, H.: Water permeation across biological membranes: Mechanism and dynamics of Aquaporin-1 and GlpF. Science 294, pp. 2353 - 2357 (2001)

Heymann, J. B.; Pfeiffer, M.; Hildebrandt, V.; Kaback, H. R.; Fotiadis, D.; de Groot, B. L.; Engel, A.; Oesterhelt, D.; Müller, D. J.: Conformations of the rhodopsin third cytoplasmic loop grafted onto bacteriorhodopsin. Structure with Folding and Design 8 (6), pp. 643 - 653 (2000)

de Groot, B. L.; Heymann, B.; Engel, A.; Mitsuoka, K.; Fujiyoshi, Y.; Grubmueller, H.: The fold of human Aquaporin 1. Journal of Molecular Biology 300, pp. 987 - 994 (2000)

Ossig, R.; Schmitt, H. D.; de Groot, B. L.; Riedel, D.; Keraenen, S.; Ronne, H.; Grubmueller, H.; Jahn, R.: Exocytosis requires asymmetry in the central layer of the SNARE complex. EMBO Journal 19, pp. 6000 - 6010 (2000)

Stahlberg, H.; Braun, T.; de Groot, B. L.; Philippsen, A.; Borgnia, M. J.; Agre, P.; Kuehlbrandt, W.; Engel, A.: The 6.9Å Structure of GlpF: A Basis for Homology Modeling of the Glycerol Channel from Escherichia coli. Journal of Structural Biology 132, pp. 133 - 141 (2000)

de Groot, B. L.; Vriend, G.; Berendsen, H. J. C.: Conformational changes in the chaperonin GroEL: New insights into the allosteric mechanism. Journal of Molecular Biology 286 (4), pp. 1241 - 1249 (1999)

van Aalten, D. M. F.; de Groot, B. L.; Berendsen, H. J. C.; Findlay, J. B. C.; Amadei, A.: A comparison of techniques for calculating protein essential dynamics. Journal of Computational Chemistry 18 (2), pp. 169 - 181 (1998)

Aldeghi, M.; de Groot, B. L.; Gapsys, V.: Accurate calculation of free energy changes upon amino acid mutation. In: Computational Methods in Protein Evolution, pp. 19 - 47 (Ed. Sikosek, T.). Springer Nature, New York (2019)

Kubitzki, M. B.; de Groot, B. L.; Seeliger, D.: Protein dynamics: From structure to function. In: From protein structure to function with bioinformatics, pp. 393 - 425 (Ed. Rigden, D. J.). Springer, Dordrecht (2017)

Gapsys, V.; Michielssens, S.; Peters, J. H.; de Groot, B.; Leonov, H.: Calculation of binding free energies. In: Molecular Modeling of Proteins, pp. 173 - 209 (Ed. Kukol, A.). Humana Pr.; Springer, New York, N.Y. (2015)

Hub, J.; Grubmuller, H.; de Groot, B. L.: Dynamics and energetics of permeation through aquaporins. What do we learn from molecular dynamics simulations? In: Aquaporins, pp. 57 - 76 (Ed. Beitz, E.). Springer, Berlin (2009)

Kubitzki, M. B.; de Groot, B. L.; Seeliger, D.: Protein dynamics: From structure to function. In: From Protein Structure to Function with Bioinformatics, pp. 217 - 249 (Ed. Rigden, D.J.). Springer, Dordrecht (2009)

Hayward, S.; de Groot, B. L.: Normal modes and essential dynamics. In: Molecular modeling of proteins, pp. 89 - 106 (Ed. Kukol, A.). Humana Pr., Totowa, N. Y. (2008)

Kutzner, C.; van der Spoel, D.; Fechner, M.; Lindahl, E.; Schmitt, U. W.; de Groot, B. L.; Grubmueller, H.: Improved GROMACS scaling on ethernet switched clusters. In: Recent advances in parallel virtual machine and message passing interface. 13th European PVM/MPI User`s Group meeting, Bonn, Germany, September 17-20, 2006, pp. 404 - 405 (Eds. Mohr, B.; Larsson, T. J.; Worringen, J.; Dongarra, J.). Springer, Berlin (2006)

Vowinkel, K. S.; Rinne, S.; Kopec, W.; Leonhardt, J.; Bedoya, M.; Schewe, M.; Kiper, A. K.; Baukrowitz, T.; Gonzalez, W.; de Groot, B. L. et al.; Decher, N.: The 'cap' structure provides an essential structural requirement for the stabilization of the K plus -flux gated open state of K2P channels. 98th Meeting of the German Physiological Society, Ulm, September 30, 2019 - October 02, 2019. Acta Physiologica 227 (719), B 06-7, (2019)

de Groot, B.: Molecular dynamics of potassium channel permeation, selectivity, and gating. National Meeting of the American-Chemical-Society (ACS), Orlando, FL, March 31, 2019 - April 04, 2019. Abstracts of Papers - American Chemical Society 257, 77, (2019)

Briones, R.; Blau, C.; Kutzner, C.; de Groot, B. L.; Aponte-Santamaria, C.: Gromaps: A Gromacs-based toolset to analyse density maps derived from molecular dynamics simulations. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, March 02, 2019 - March 06, 2019. Biophysical Journal 116 (Suppl_1), pp. 142A - 143A (2019)

Kopec, W.; de Groot, B. L.: Molecular simulations of ion permeation, gating and selectivity in K⁺ channels. 63rd Annual Meeting of the Biophysical-Society, Baltimore, MD, March 02, 2019 - March 06, 2019. Biophysical Journal 116 (Suppl_1), p. 16A - 16A (2019)