Publications of the Department (MPG.PuRe list)

101.

Journal Article

Hett, T.; Zbik, T.; Mukherjee, S.; Matsuoka, H.; Bönigk, W.; Klose, D.; Rouillon, C.; Brenner, N.; Peuker, S.; Klement, R. et al.; Steinhoff, H.-J.; Grubmüller, H.; Seifert, R.; Schiemann, O.; Kaupp, U. B.: Spatiotemporal resolution of conformational changes in biomolecules by combining pulsed electron–electron double resonance spectroscopy with microsecond freeze-hyperquenching. Journal of the American Chemical Society 143 (18), pp. 6981 - 6989 (2021)

MPG.PuRe

102.

Journal Article

Gapsys, V.; Yildirim, A.; Aldeghi, M.; Khalak, Y.; van der Spoel, D.; de Groot, B. L.: Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches. Communications Chemistry 4, 61 (2021)

MPG.PuRe

103.

Journal Article

Roy, R. N.; Hendriks, K.; Kopec, W.; Abdolvand, S.; Weiss, K. L.; de Groot, B. L.; Lange, A.; Sun, H.; Coates, L.: Structural plasticity of the selectivity filter in a nonselective ion channel. IUCrJ 8 (3), pp. 421 - 430 (2021)

MPG.PuRe

104.

Journal Article

Baumann, H. M.; Gapsys, V.; de Groot, B. L.; Mobley, D. L.: Challenges encountered applying equilibrium and nonequilibrium binding free energy calculations. Journal of Physical Chemistry B 125 (17), pp. 4241 - 4261 (2021)

MPG.PuRe

105.

Journal Article

Jahnke, K.; Grubmüller, H.; Igaev, M.; Göpfrich, K.: Choice of fluorophore affects dynamic DNA nanostructures. Nucleic Acids Research 49 (7), pp. 4186 - 4195 (2021)

MPG.PuRe

106.

Journal Article

Heinz, L. P.; Grubmüller, H.: Per|Mut: Spatially resolved hydration entropies from atomistic simulations. Journal of Chemical Theory and Computation 17 (4), pp. 2090 - 2098 (2021)

MPG.PuRe

107.

Journal Article

Werner, M.; Gapsys, V.; de Groot, B. L.: One plus one makes three: Triangular coupling of correlated amino acid mutations. Journal of Physical Chemistry Letters 12 (12), pp. 3195 - 3201 (2021)

MPG.PuRe

108.

Journal Article

Buelens, F. P.; Leonov, H.; de Groot, B. L.; Grubmüller, H.: ATP-magnesium coordination: Protein structure-based force field evaluation and corrections. Journal of Chemical Theory and Computation 17 (3), pp. 1922 - 1930 (2021)

MPG.PuRe

109.

Journal Article

Daday, C.; de Groot, B. L.: Lipid–protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal 50 (2), pp. 181 - 186 (2021)

MPG.PuRe

110.

Journal Article

de Groot, B. L.; Janshoff, A.; Steinem, C.; Zweckstetter, M.: Special issue: Multicomponent lipid membranes—how molecular organisation leads to function. European Biophysics Journal 50 (2), pp. 107 - 108 (2021)

MPG.PuRe

111.

Journal Article

Najbauer, E.; Becker, S.; Giller, K.; Zweckstetter, M.; Lange, A.; Steinem, C.; de Groot, B. L.; Griesinger, C.; Andreas, L. B.: Structure, gating and interactions of the voltage-dependent anion channel. European Biophysics Journal 50 (2), pp. 159 - 172 (2021)

MPG.PuRe

112.

Journal Article

Risselada, H. J.; Grubmüller, H.: How proteins open fusion pores: insights from molecular simulations. European Biophysics Journal 50 (2), pp. 279 - 293 (2021)

MPG.PuRe

113.

Journal Article

Zhang, Y.; Daday, C.; Gu, R. X.; Cox, C. D.; Martinac, B.; de Groot, B. L.; Walz, T.: Visualization of the mechanosensitive ion channel MscS under membrane tension. Nature 590 (7846), pp. 509 - 514 (2021)

MPG.PuRe

114.

Journal Article

Lawson, C. L.; Kryshtafovych, A.; Adams, P. D.; Afonine, P. V.; Baker, M. L.; Barad, B. A.; Bond, P.; Burnley, T.; Cao, R.; Cheng, J. et al.; Chojnowski, G.; Cowtan, K.; Dill, K. A.; DiMaio, F.; Farrell, D. P.; Fraser, J. S.; Herzik Jr., M. A. H.; Hoh, S. W.; Hou, J.; Hung, L.-W.; Igaev, M.; Joseph, A. P.; Kihara, D.; Kumar, D.; Mittal, S.; Monastyrskyy, B.; Olek, M.; Palmer, C. M.; Patwardhan, A.; Perez, A.; Pfab, J.; Pintilie, G. D.; Richardson, J. S.; Rosenthal, P. B.; Sarkar, D.; Schäfer, L. U.; Schmid, M. F.; Schröder, G. F.; Shekhar, M.; Si, D.; Singharoy, A.; Terashi, G.; Terwilliger, T. C.; Vaiana, A.; Wang, L.; Wang, Z.; Wankowicz, S. A.; Williams, C. J.; Winn, M.; Wu, T.; Yu, X.; Zhang, K.; Berman, H. M.; Chiu, W.: Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods 18, pp. 156 - 164 (2021)

MPG.PuRe

115.

Journal Article

Khalak, Y.; Tresadern, G.; de Groot, B. L.; Gapsys, V.: Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. Journal of Computer-Aided Molecular Design 35 (1), pp. 49 - 61 (2021)

MPG.PuRe

116.

Journal Article

Kohnke, B.; Kutzner, C.; Beckmann, A.; Lube, G.; Kabadshow, I.; Dachsel, H.; Grubmüller, H.: A CUDA fast multipole method with highly efficient M2L farfield evaluationfield evaluation. The International Journal of High Performance Computing Applications 35 (1), pp. 97 - 117 (2021)

MPG.PuRe

117.

Journal Article

Lapolla, A.; Godec, A.: BetheSF: Efficient computation of the exact tagged-particle propagator in single-file systems via the Bethe eigenspectrum. Computer Physics Communications 258, 107569 (2021)

MPG.PuRe

118.

Journal Article

Bubnis, G.; Grubmüller, H.: Sequential water and headgroup merger: Membrane poration paths and energetics from MD simulations. Biophysical Journal 119 (12), pp. 2418 - 2430 (2020)

MPG.PuRe

119.

Journal Article

Kolar, M. H.; Bock, L. V.; Grubmüller, H.: Atomistic simulations of the human proteasome inhibited by a covalent ligand. arXiv, 2012.03387 (2020)

MPG.PuRe

120.

Journal Article

Lapolla, A.; Hartich, D.; Godec, A.: Spectral theory of fluctuations in time-average statistical mechanics of reversible and driven systems. Physical Review Research 2 (4), 043084 (2020)

MPG.PuRe

121.

Journal Article

Lapolla, A.; Godec, A.: Single-file diffusion in a bi-stable potential: Signatures of memory in the barrier-crossing of a tagged-particle. The Journal of Chemical Physics 153 (19), 194104 (2020)

MPG.PuRe

122.

Journal Article

Kohnke, B.; Kutzner, C.; Grubmüller, H.: A GPU-accelerated fast multipole method for GROMACS: Performance and accuracy. Journal of Chemical Theory and Computation 16 (11), pp. 6938 - 6949 (2020)

MPG.PuRe

123.

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 16 (11), p. 1237-1245 (2020)

MPG.PuRe

124.

Journal Article

Reinhardt, M.; Grubmüller, H.: Variationally derived intermediates for correlated free-energy estimates between intermediate states. Physical Review E 102 (4), 043312 (2020)

MPG.PuRe

125.

Journal Article

Lapolla, A.; Godec, A.: Faster uphill relaxation in thermodynamically equidistant temperature quenches. Physical Review Letters 125 (11), 110602 (2020)

MPG.PuRe

126.

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)

MPG.PuRe

127.

Journal Article

Igaev, M.; Grubmüller, H.: Microtubule instability driven by longitudinal and lateral strain propagation. PLoS Computational Biology 16 (9), e1008132 (2020)

MPG.PuRe

128.

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)

MPG.PuRe

129.

Journal Article

Nagy, G.; Grubmueller, H.: How accurate is circular dichroism-based model validation? European Biophysics Journal 49 (6), pp. 497 - 510 (2020)

MPG.PuRe

130.

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)

MPG.PuRe

131.

Journal Article

Ukmar-Godec, T.; Fang, P.; Ibáñez de Opakua, A.; Henneberg, F.; Godec, A.; Pan, K. T.; Cima-Omori, M.-S.; Chari, A.; Mandelkow, E.; Urlaub, H. et al.; Zweckstetter, M.: Proteasomal degradation of the intrinsically disordered protein tau at single-residue resolution. Science Advances 6 (30), eaba3916 (2020)

MPG.PuRe

132.

Journal Article

Reinhardt, M.; Grubmüller, H.: Determining free-energy differences through variationally derived intermediates. Journal of Chemical Theory and Computation 16 (6), pp. 3504 - 3512 (2020)

MPG.PuRe

133.

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)

MPG.PuRe

134.

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)

MPG.PuRe

135.

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 34 (5), pp. 601 - 633 (2020)

MPG.PuRe

136.

Journal Article

Dobrev, P.; Vemulapalli, S. P.; Nath, N.; Griesinger, C.; Grubmüller, H.: Probing the accuracy of explicit solvent constant pH molecular dynamics simulations for peptides. Journal of Chemical Theory and Computation 16 (4), pp. 2561 - 2569 (2020)

MPG.PuRe

137.

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)

MPG.PuRe

138.

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)

MPG.PuRe

139.

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)

MPG.PuRe

140.

Journal Article

Warias, M.; Grubmüller, H.; Bock, L. V.: tRNA dissociation from EF-Tu after GTP hydrolysis: Primary steps and antibiotic inhibition. Biophysical Journal 118 (1), pp. 151 - 161 (2020)

MPG.PuRe

141.

Journal Article

Heinz, L. P.; Grubmüller, H.: Computing spatially resolved rotational hydration entropies from atomistic simulations. Journal of Chemical Theory and Computation 16 (1), pp. 108 - 118 (2020)

MPG.PuRe

142.

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 (1), pp. 27 - 43 (2020)

MPG.PuRe

143.

Journal Article

Peng, B. Z.; Bock, L. V.; Belardinelli, R.; Peske, F.; Grubmüller, H.; Rodnina, M. V.: Active role of elongation factor G in maintaining the mRNA reading frame during translation. Science Advances 5 (12), eaax8030 (2019)

MPG.PuRe

144.

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)

MPG.PuRe

145.

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)

MPG.PuRe

146.

Journal Article

Lapolla, A.; Godec, A.: Manifestations of projection-induced memory: General theory and the tilted single file. Frontiers in Physics 7, 182 (2019)

MPG.PuRe

147.

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)

MPG.PuRe

148.

Journal Article

Bock, L. V.; Caliskan, N.; Korniy, N.; Peske, F.; Rodnina, M. V.; Grubmüller, H.: Thermodynamic control of −1 programmed ribosomal frameshifting. Nature Communications 10, 4598 (2019)

MPG.PuRe

149.

Journal Article

Nagy, G.; Igaev, M.; Hoffmann, S. V.; Jones, N. C.; Grubmüller, H.: SESCA: Predicting circular dichroism spectra from protein molecular structures. Journal of Chemical Theory and Computation 15 (9), pp. 5087 - 5102 (2019)

MPG.PuRe

150.

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)

MPG.PuRe

151.

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)

MPG.PuRe

152.

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)

MPG.PuRe

153.

Journal Article

Hartich, D.; Godec, A.: Extreme value statistics of ergodic Markov processes from first passage times in the large deviation limit. Journal of Physics A: Mathematical and Theoretical 52, 244001 (2019)

MPG.PuRe

154.

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)

MPG.PuRe

155.

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)

MPG.PuRe

156.

Journal Article

Rico, F.; Russek, A.; Gonzalez, L.; Grubmüller, H.; Scheuring, S.: Heterogeneous and rate-dependent streptavidin-biotin unbinding revealed by high-speed force spectroscopy and molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America 116 (14), pp. 6594 - 6601 (2019)

MPG.PuRe

157.

Journal Article

Rico, F.; Russek, A.; González, L.; Grubmüller, H.; Scheuring, S.: Heterogeneous and rate-dependent streptavidin–biotin unbinding revealed by high-speed force spectroscopy and atomistic simulations. Proceedings of the National Academy of Sciences of the United States of America 116 (14), pp. 6594 - 6601 (2019)

MPG.PuRe

158.

Journal Article

Igaev, M.; Kutzner, C.; Bock, L. V.; Vaiana, A. C.; Grubmüller, H.: Automated cryo-EM structure refinement using correlation-driven molecular dynamics. eLife 8, e43542 (2019)

MPG.PuRe

159.

Journal Article

Hartich, D.; Godec, A.: Interlacing relaxation and first-passage phenomena in reversible discrete and continuous space Markovian dynamics. Journal of Statistical Mechanics: Theory and Experiment 2019, 024002 (2019)

MPG.PuRe

160.

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)

MPG.PuRe

161.

Journal Article

Schewe, M.; Sun, H.; Mert, Ü.; Mackenzie, A.; Pike, A. C. W.; Schulz, F.; Constantin, C.; Vowinkel, K. S.; Conrad, L. J.; Kiper, A. K. et al.; Gonzalez, W.; Musinszki, M.; Tegtmeier, M.; Pryde, D. C.; Belabed, H.; Nazare, M.; de Groot, B. L.; Decher, N.; Fakler, B.; Carpenter, E. P.; Tucker, S. J.; Baukrowitz, T.: A pharmacological master key mechanism that unlocks the selectivity filter gate in K⁺ channels. Science 363 (6429), pp. 875 - 880 (2019)

MPG.PuRe

162.

Journal Article

Awasthi, N.; Kopec, W.; Wilkosz, N.; Jamroz, D.; Hub, J. S.; Zatorska, M.; Petka, R.; Nowakowska, M.; Kepczynski, M.: Molecular mechanism of polycation-induced pore formation in biomembranes. ACS Biomaterials Science and Engineering 5 (2), pp. 780 - 794 (2019)

MPG.PuRe

163.

Journal Article

Cordeiro, S.; Finol-Urdaneta, R. K.; Köpfer, D.; Markushina, A.; Song, J.; French, R. J.; Kopec, W.; de Groot, B. L.; Giacobassi, M. J.; Leavitt, L. S. et al.; Raghuraman, S.; Teichert, R. W.; Olivera, B. M.; Terlau, H.: Conotoxin κM-RIIIJ, a tool targeting asymmetric heteromeric K_v1 channels. Proceedings of the National Academy of Sciences of the United States of America 116 (3), pp. 1059 - 1064 (2019)

MPG.PuRe

164.

Journal Article

Briones, R.; Blau, C.; Kutzner, C.; de Groot, B. L.; Aponte-Santamaría, C.: GROmaρs: A GROMACS-based toolset to analyze density maps derived from molecular dynamics simulations. Biophysical Journal 116 (1), pp. 4 - 11 (2019)

MPG.PuRe

165.

Journal Article

Lutz, H.; Jaeger, V.; Weidner, T.; de Groot, B. L.: Interpretation of interfacial protein spectra with enhanced molecular simulation ensembles. Journal of Chemical Theory and Computation 15 (1), pp. 698 - 707 (2019)

MPG.PuRe

166.

Journal Article

Abraham, M. J.; Apostolov, R. P.; Barnoud, J.; Bauer, P.; Blau, C.; Bonvin, A. M. J. J.; Chavent, M.; Chodera, J. D.; Čondić-Jurkić, K.; Delemotte, L. et al.; Grubmüller, H.; Howard, R. J.; Jordan, E. J.; Lindal, E.; Ollila, O. H. S.; Selent, J.; Smith, D. G. A.; Stansfeld, P. J.; Tiemann, J. K. S.; Trellet, M.; Woods, C. J.; Zhmurov, A.: Sharing data from molecular simulations. Journal of Chemical Information and Modeling 59 (10), pp. 4093 - 4099 (2019)

MPG.PuRe

167.

Journal Article

Gu, R. X.; Baoukina, S.; Tieleman, D. P.: Cholesterol flip-flop in heterogeneous membranes. Journal of Chemical Theory and Computation 15 (3), pp. 2064 - 2070 (2019)

MPG.PuRe

168.

Journal Article

Paul, F.; Wu, H.; Vossel, M.; de Groot, B. L.; Noé, F.: Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics 150 (16), 164120 (2019)

MPG.PuRe

169.

Journal Article

Rovo, P.; Smith, C. A.; Gauto, D.; de Groot, B. L.; Schanda, P.; Linser, R.: Mechanistic insights into microsecond time-scale motion of solid proteins using complementary ¹⁵N and ¹H relaxation dispersion techniques. Journal of the American Chemical Society 141 (2), pp. 858 - 869 (2019)

MPG.PuRe

170.

Journal Article

Aldeghi, M.; Gapsys, V.; de Groot, B. L.: Accurate estimation of ligand binding affinity changes upon protein mutation. ACS Central Science 4 (12), pp. 1708 - 1718 (2018)

MPG.PuRe

171.

Journal Article

Hartich, D.; Godec, A.: Duality between relaxation and first passage in reversible Markov dynamics: Rugged energy landscapes disentangled. New Journal of Physics 20 (11), 112002 (2018)

MPG.PuRe

172.

Journal Article

Lapolla, A.; Godec, A.: Unfolding tagged particle histories in single-file diffusion: Exact single- and two-tag local times beyond large deviation theory. New Journal of Physics 20, 113021 (2018)

MPG.PuRe

173.

Journal Article

Graen, T.; Klement, R.; Grupi, A.; Haas, E.; Grubmüller, H.: Transient secondary and tertiary structure formation kinetics in the intrinsically disordered state of α-Synuclein from atomistic simulations. ChemPhysChem 19 (19), pp. 2507 - 2511 (2018)

MPG.PuRe

174.

Journal Article

Brennecke, J. T.; de Groot, B. L.: Quantifying asymmetry of multimeric proteins. The Journal of Physical Chemistry A 122 (39), pp. 7924 - 7930 (2018)

MPG.PuRe

175.

Journal Article

Bassereau, P.; Jin, R.; Baumgart, T.; Deserno, M.; Dimova, R.; Frolov, V. A.; Bashkirov, P. V.; Grubmüller, H.; Jahn, R.; Risselada, H. J. et al.; Johannes, L.; Kozlov, M. M.; Lipowsky, R.; Pucadyil, T. J.; Zeno, W. F.; Stachowiak, J. C.; Stamou, D.; Breuer, A.; Lauritsen, L.; Simon, C.; Sykes, C.; Voth, G. A.; Weikl, T. R.: The 2018 biomembrane curvature and remodeling roadmap. Journal of Physics D: Applied Physics 51 (34), 343001 (2018)

MPG.PuRe

176.

Journal Article

Kopec, W.; Köpfer, D.; Vickery, O. N.; Bondarenko, A. S.; Jansen, T. L. C.; de Groot, B. L.; Zachariae, U.: Direct knock-on of desolvated ions governs strict ion selectivity in K⁺ channels. Nature Chemistry 10 (8), pp. 813 - 820 (2018)

MPG.PuRe

177.

Journal Article

Bastys, T.; Gapsys, V.; Doncheva, N. T.; Kaiser, R.; de Groot, B. L.; Kalinina, O. V.: Consistent prediction of mutation effect on drug binding in HIV-1 protease using alchemical calculations. Journal of Chemical Theory and Computation 14 (7), pp. 3397 - 3408 (2018)

MPG.PuRe

178.

Journal Article

von Ardenne, B.; Mechelke, M.; Grubmüller, H.: Structure determination from single molecule X-ray scattering with three photons per image. Nature Communications 9, 2375 (2018)

MPG.PuRe

179.

Journal Article

Rydzewski, J.; Jakubowski, R.; Nowak, W.; Grubmüller, H.: Kinetics of huperzine A dissociation from acetylcholinesterase via multiple unbinding pathways. Journal of Chemical Theory and Computation 14 (6), pp. 2843 - 2851 (2018)

MPG.PuRe

180.

Journal Article

Heinz, L. P.; Kopec, W.; de Groot, B. L.; Fink, R. H. A.: In silico assessment of the conduction mechanism of the ryanodine receptor 1 reveals previously unknown exit pathways. Scientific Reports 8, 6886 (2018)

MPG.PuRe

181.

Journal Article

Igaev, M.; Grubmüller, H.: Microtubule assembly governed by tubulin allosteric gain in flexibility and lattice induced fit. eLife 7, e34353 (2018)

MPG.PuRe

182.

Journal Article

Bock, L. V.; Kolar, M. H.; Grubmüller, H.: Molecular simulations of the ribosome and associated translation factors. Current Opinion in Structural Biology 49, pp. 27 - 35 (2018)

MPG.PuRe

183.

Journal Article

Sabo, T. M.; Gapsys, V.; Walter, K. F. A.; Fenwick, R. B.; Becker, S.; Salvatella, X.; de Groot, B. L.; Lee, D.; Griesinger, C.: Utilizing dipole-dipole cross-correlated relaxation for the measurement of angles between pairs of opposing CαHα-CαHα bonds in anti-parallel β-sheets. Methods 138-139, pp. 85 - 92 (2018)

MPG.PuRe

184.

Journal Article

Brennecke, J. T.; de Groot, B. L.: Mechanism of mechanosensitive gating of the TREK-2 potassium channel. Biophysical Journal 114 (6), pp. 1336 - 1343 (2018)

MPG.PuRe

185.

Journal Article

Shi, C.; He, Y.; Hendriks, K.; de Groot, B. L.; Cai, X.; Tian, C.; Lange, A.; Sun, H.: A single NaK channel conformation is not enough for non-selective ion conduction. Nature Communications 9, 717 (2018)

MPG.PuRe

186.

Journal Article

Matthes, D.; Gapsys, V.; Griesinger, C.; de Groot, B. L.: Resolving the atomistic modes of anle138b inhibitory action on peptide oligomer formation. ACS Chemical Neuroscience 8 (12), pp. 2791 - 2808 (2017)

MPG.PuRe

187.

Journal Article

Gapsys, V.; de Groot, B. L.: Alchemical free energy calculations for nucleotide mutations in protein-DNA complexes. Journal of Chemical Theory and Computation 13 (12), pp. 6275 - 6289 (2017)

MPG.PuRe

188.

Journal Article

Bock, L. V.; Kolář, M. H.; Grubmüller, H.: Molecular simulations of the ribosome and associated translation factors. arXiv, arXiv:1711.06067 (2017)

MPG.PuRe

189.

Journal Article

Huter, P.; Arenz, S.; Bock, L. V.; Graf, M.; Frister, J. O.; Heuer, A.; Peil, L.; Starosta, A. L.; Wohlgemuth, I.; Peske, F. et al.; Nováček, J.; Berninghausen, O.; Grubmüller, H.; Tenson, T.; Beckmann, R.; Rodnina, M. V.; Vaiana, A. C.; Wilson, D. N.: Structural basis for polyproline-mediated ribosome stalling and rescue by the translation elongation factor EF-P. Molecular Cell 68 (3), pp. 515 - 527 (2017)

MPG.PuRe

190.

Journal Article

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