Publikationen

Zeitschriftenartikel (9714)

1.
Zeitschriftenartikel
Lapolla, A.; Godec, A.: BetheSF V2: 3-point propagator and additional external potentials. Computer Physics Communications 269, 108131 (2021)
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2.
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Lapolla, A.; Vossel, M.; Godec, A.: Time- and ensemble-average statistical mechanics of the Gaussian network model. Journal of Physics A 54 (35), 355601 (2021)
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3.
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Bhatta, A.; Dienemann, C.; Cramer, P.; Hillen, H.: Structural basis of RNA processing by human mitochondrial RNase P. Nature Structural and Molecular Biology 28 (9), S. 713 - 723 (2021)
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4.
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Nagy, G.; Grubmüller, H.: Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package. Computer Physics Communications 266, 108022 (2021)
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5.
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Fingerhut, J.; Borodin, D.; Schwarzer, M.; Skoulatakis, G.; Auerbach, D. J.; Wodtke, A. M.; Kitsopoulos, T. N.: The barrier for CO2 functionalization to formate on hydrogenated Pt. Journal of Physical Chemistry A 125 (34), S. 7396 - 7405 (2021)
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6.
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Jochheim, F. A.; Tegunov, D.; Hillen, H. S.; Schmitzova, J.; Kokic, G.; Dienemann, C.; Cramer, P.: The structure of a dimeric form of SARS-CoV-2 polymerase. Communications Biology 4, 999 (2021)
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7.
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Borodin, D.; Schwarzer, M.; Hahn, H. W.; Fingerhut, J.; Wang, Y.; Auerbach, D. J.; Guo, H.; Schroeder, J.; Kitsopoulos, T. N.; Wodtke, A. M.: The puzzle of rapid hydrogen oxidation on Pt(111). Molecular Physics, In Press; e1966533 (2021)
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8.
Zeitschriftenartikel
Hartich, D.; Godec, A.: Thermodynamic uncertainty relation bounds the extent of anomalous diffusion. Physical Review Letters 127 (8), 080601 (2021)
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9.
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Nair, R. M.; Seenivasan, A.; Liu, B.; Chen, D.; Lowe, E. D.; Lorenz, S.: Reconstitution and structural analysis of a HECT ligase-ubiquitin complex via an activity-based probe. ACS Chemical Biology, In Press (2021)
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10.
Zeitschriftenartikel
Kabinger, F.; Stiller, C.; Schmitzova, J.; Dienemann, C.; Kokic, G.; Hillen, H. S.; Höbartner, C.; Cramer, P.: Mechanism of molnupiravir-induced SARS-CoV-2 mutagenesis. Nature Structural and Molecular Biology, In Press (2021)
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11.
Zeitschriftenartikel
Quan, J.; Chang, Y.; Li, Z.; Zhao, Y.; Luo, Z.; Wu, Y.; Zhang, S.; Chen, Z.; Yang, J.; Yuan, K. et al.; Yang, X.; Krüger, B. C.; Schwarzer, D.; Wodtke, A. M.; Park, G. B.: A free electron laser-based 1+1′ resonance-enhanced multiphoton ionization scheme for rotationally resolved detection of OH radicals with correct relative intensities. Journal of Molecular Spectroscopy 380, 111509 (2021)
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12.
Zeitschriftenartikel
Wang, H.; Xiong, L.; Cramer, P.: Structures and implications of TBP–nucleosome complexes. Proceedings of the National Academy of Sciences of the USA 118 (30), e2108859118 (2021)
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13.
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Schilbach, S.; Aibara, S.; Dienemann, C.; Grabbe, F.; Cramer, P.: Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening. Cell 184 (15), S. 4064 - 4072.e28 (2021)
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14.
Zeitschriftenartikel
King, A. J.; Songdej, D.; Downes, D. J.; Beagrie, R. A.; Liu, S.; Buckley, M.; Hua, P.; Suciu, M. C.; Oudelaar, A. M.; Hanssen, L. L. P. et al.; Jeziorska, D.; Roberts, N.; Carpenter, S. J.; Francis, H.; Telenius, J.; Olijnik, A.-A.; Sharpe, J. A.; Sloane-Stanley, J.; Eglinton, J.; Kassouf, M. T.; Orkin, S. H.; Pennacchio, L. A.; Davies, J. O. J.; Hughes, J. R.; Higgs, D. R.; Babbs, C.: Reactivation of a developmentally silenced embryonic globin gene. Nature Communications 12, 4439 (2021)
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15.
Zeitschriftenartikel
Lecroart, L.; Hertl, N.; Dorenkamp, Y.; Jiang, H.; Kitsopoulos, T. N.; Kandratsenka, A.; Bünermann, O.; Wodtke, A. M.: Adsorbate modification of electronic nonadiabaticity: H atom scattering from p(2 × 2) O on Pt(111). The Journal of Chemical Physics 155 (3), 034702 (2021)
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16.
Zeitschriftenartikel
García-Martínez, J.; Medina, D. A.; Bellvís, P.; Sun, M.; Cramer, P.; Chávez, S.; Pérez-Ortín, J. E.: The total mRNA concentration buffering system in yeast is global rather than gene-specific. RNA, In Press (2021)
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17.
Zeitschriftenartikel
Chen, Y.; Vos, S. M.; Dienemann, C.; Ninov, M.; Urlaub, H.; Cramer, P.: Allosteric transcription stimulation by RNA polymerase II super elongation complex. Molecular Cell 81 (16), S. 3386 - 3399.e10 (2021)
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18.
Zeitschriftenartikel
Huang, X.; Hu, H.; Webster, A.; Zou, F.; Du, J.; Patel, D. J.; Sachidanandam, R.; Toth, K. F.; Aravin, A. A.; Li, S.: Binding of guide piRNA triggers methylation of the unstructured N-terminal region of Aub leading to assembly of the piRNA amplification complex. Nature Communications 12, 4061 (2021)
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19.
Zeitschriftenartikel
Reinhardt, M.; Grubmüller, H.: GROMACS implementation of free energy calculations with non-pairwise variationally derived intermediates. Computer Physics Communications 264, 107931 (2021)
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20.
Zeitschriftenartikel
Ng, S. C.; Güttler, T.; Görlich, D.: Recapitulation of selective nuclear import and export with a perfectly repeated 12mer GLFG peptide. Nature Communications 12, 4047 (2021)
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21.
Zeitschriftenartikel
Orth, B.; Sander, B.; Möglich, A.; Diederichs, K.; Eilers, M.; Lorenz, S.: Identification of an atypical interaction site in the BTB domain of the MYC-interacting zinc-finger protein 1. Structure, In Press (2021)
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22.
Zeitschriftenartikel
Bozhilov, Y. K.; Downes, D. J.; Telenius, J.; Oudelaar, A. M.; Olivier, E. N.; Mountford, J. C.; Hughes, J. R.; Gibbons, R. J.; Higgs, D. R.: A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker. Nature Communications 12, 3806 (2021)
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23.
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Zumer, K.; Maier, K. C.; Farnung, L.; Jaeger, M. G.; Rus, P.; Winter, G.; Cramer, P.: Two distinct mechanisms of RNA polymerase II elongation stimulation in vivo. Molecular Cell, In Press (2021)
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24.
Zeitschriftenartikel
Hua, P.; Badat, M.; Hanssen, L. L. P.; Hentges, L. D.; Crump, N.; Downes, D. J.; Jeziorska, D. M.; Oudelaar, A. M.; Schwessinger, R.; Taylor, S. et al.; Milne, T. A.; Hughes, J. R.; Higgs, D. R.; Davies, J. O. J.: Defining genome architecture at base-pair resolution. Nature, In Press (2021)
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25.
Zeitschriftenartikel
Aibara, S.; Schilbach, S.; Cramer, P.: Structures of mammalian RNA polymerase II pre-initiation complexes. Nature 594 (7861), S. 124 - 128 (2021)
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26.
Zeitschriftenartikel
Witkowska, A.; Heinz, L. P.; Grubmüller, H.; Jahn, R.: Tight docking of membranes before fusion represents a novel, metastable state with unique properties. Nature Communications (angenommen)
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27.
Zeitschriftenartikel
Lapolla, A.; Godec, A.: Toolbox for quantifying memory in dynamics along reaction coordinates. Physical Review Research 3 (2), L022018 (2021)
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28.
Zeitschriftenartikel
Oberbeckmann, E.; Niebauer, V.; Watanabe, S.; Farnung, L.; Moldt, M.; Schmid, A.; Cramer, P.; Peterson, C. L.; Eustermann, S.; Hopfner, K.-P. et al.; Korber, P.: Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nature Communications 12, 3232 (2021)
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29.
Zeitschriftenartikel
Fianu, I.; Dienemann, C.; Aibara, S.; Schilbach, S.; Cramer, P.: Cryo-EM structure of mammalian RNA polymerase II in complex with human RPAP2. Communications Biology 4, 606 (2021)
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30.
Zeitschriftenartikel
Quentin, C.; Gerasimaite, R.; Freidzon, A.; Atabekyan, L. S.; Lukinavičius, G.; Belov, V. N.; Mitronova, G.: Direct visualization of amlodipine intervention into living cells by means of fluorescence microscopy. Molecules 26 (10), 2997 (2021)
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31.
Zeitschriftenartikel
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), S. 6981 - 6989 (2021)
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32.
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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)
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33.
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Cavazza, T.; Takeda, Y.; Politi, A.; Aushev, M.; Aldag, P.; Baker, C.; Choudhary, M.; Bucevičius, J.; Lukinavičius, G.; Elder, K. et al.; Blayney, M.; Lucas-Hahn, A.; Niemann, H.; Herbert, M.; Schuh, M.: Parental genome unification is highly error-prone in mammalian embryos. Cell, In Press (2021)
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34.
Zeitschriftenartikel
Hecker, F.; Stubbe, J.; Bennati, M.: Detection of water molecules on the radical transfer pathway of ribonucleotide reductase by 17O electron–nuclear double resonance spectroscopy. The Journal of the American Chemical Society, In Press (2021)
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35.
Zeitschriftenartikel
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), S. 4241 - 4261 (2021)
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36.
Zeitschriftenartikel
Rengachari, S.; Schilbach, S.; Aibara, S.; Dienemann, C.; Cramer, P.: Structure of human Mediator-RNA polymerase II pre-initiation complex. Nature, In Press (2021)
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37.
Zeitschriftenartikel
Uno, K.; Aktalay, A.; Bossi, M. L.; Irie, M.; Belov, V. N.; Hell, S. W.: Turn-on mode diarylethenes for bioconjugation and fluorescence microscopy of cellular structures. Proceedings of the National Academy of Sciences of the USA 118 (14), e2100165118 (2021)
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38.
Zeitschriftenartikel
Farnung, L.; Ochmann, M.; Engeholm, M.; Cramer, P.: Structural basis of nucleosome transcription mediated by Chd1 and FACT. Nature Structural and Molecular Biology 28 (4), S. 382 - 387 (2021)
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39.
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Oudelaar, A. M.; Beagrie, R. A.; Kassouf, M. T.; Higgs, D. R.: The mouse alpha-globin cluster: A paradigm for studying genome regulation and organization. Current Opinion in Genetics and Development 67, S. 18 - 24 (2021)
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40.
Zeitschriftenartikel
So, C.; Cheng, S.; Schuh, M.: Phase separation during germline development. Trends in Cell Biology 31 (4), S. 254 - 268 (2021)
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41.
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Choi, J.; Lysakovskai, K.; Lysakovskaia, K.; Stik, G.; Demel, C.; Söding, J.; Tian, T. V.; Graf, T.; Cramer, P.: Evidence for additive and synergistic action of mammalian enhancers during cell fate determination. eLife 10, e65381 (2021)
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42.
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Medina, L.; González-Lizárraga, F.; Dominguez-Meijide, A.; Ploper, D.; Parrales, V.; Sequeira, S.; Cima-Omori, M.-S.; Zweckstetter, M.; Bel, E. D.; Michel, P. P. et al.; Outeiro, T. F.; Raisman-Vozari, R.; Chehín, R.; Socias, S. B.: Doxycycline Interferes With Tau Aggregation and Reduces Its Neuronal Toxicity. Frontiers in Aging Neuroscience 13, 635760 (2021)
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43.
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Butola, T.; Alvanos, T.; Hintze, A.; Koppensteiner, P.; Kleindienst, D.; Shigemoto, R.; Wichmann, C.; Moser, T.: RIM-Binding Protein 2 organizes Ca2+channel topography and regulates release probability and vesicle replenishment at a fast central synapse. bioRxiv, 435607 (2021)
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44.
Zeitschriftenartikel
Weber, M.; Leutenegger, M.; Stoldt, S.; Jakobs, S.; Mihaila, T. S.; Butkevich, A. N.; Hell, S. W.: MINSTED fluorescence localization and nanoscopy. Nature Photonics 15, S. 361 - 366 (2021)
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45.
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Heinz, L. P.; Grubmüller, H.: Per|Mut: Spatially resolved hydration entropies from atomistic simulations. Journal of Chemical Theory and Computation, In Press (2021)
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46.
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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), S. 1922 - 1930 (2021)
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47.
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Caizzi, L.; Monteiro-Martins, S.; Schwalb, B.; Lysakovskaya, K.; Schmitzova, J.; Sawicka, A.; Chen, Y.; Lidschreiber, M.; Cramer, P.: Efficient RNA polymerase II pause release requires U2 snRNP function. Molecular Cell, In Press (2021)
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48.
Zeitschriftenartikel
Larke, M. S. C.; Schwessinger, R.; Nojima, T.; Telenius, J.; Beagrie, R. A.; Downes, D. J.; Oudelaar, A. M.; Truch, J.; Graham, B.; Bender, M. A. et al.; Proudfoot, N. J.; Higgs, D. R.; Hughes, J. R.: Enhancers predominantly regulate gene expression during differentiation via transcription initiation. Molecular Cell 81 (5), S. 983 - 997.e7 (2021)
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49.
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Rawat, P.; Böhning, M.; Hummel, B.; Aprile-Garcia, F.; Pandit, A. S.; Eisenhardt, N.; Khavaran, A.; Niskanen, E.; Vos, S. M.; Palvimo, J. J. et al.; Pichler, A.; Cramer, P.; Sawarkar, R.: Stress-induced nuclear condensation of NELF drives transcriptional downregulation. Molecular Cell 81 (5), S. 1013 - 1026.e11 (2021)
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50.
Zeitschriftenartikel
Daday, C.; de Groot, B. L.: Lipid–protein forces predict conformational changes in a mechanosensitive channel. European Biophysics Journal 50 (2), S. 181 - 186 (2021)
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51.
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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), S. 107 - 108 (2021)
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52.
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Grothe, T.; Nowak, J.; Jahn, R.; Walla, P. J.: Selected tools to visualize membrane interactions. European Biophysics Journal 50 (2), S. 211 - 222 (2021)
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53.
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Kroppen, B.; Teske, N.; Yambire, K. F.; Denkert, N.; Mukherjee, I.; Tarasenko, D.; Jaipuria, G.; Zweckstetter, M.; Milosevic, I.; Steinem, C. et al.; Meinecke, M.: Cooperativity of membrane-protein and protein–protein interactions control membrane remodeling by epsin 1 and affects clathrin-mediated endocytosis. Cellular and Molecular Life Sciences 78 (5), S. 2355 - 2370 (2021)
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54.
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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), S. 159 - 172 (2021)
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55.
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Özçete, Ö. D.; Moser, T.: A sensory cell diversifies its output by varying Ca2+ influx‐release coupling among active zones. EMBO Journal 40 (5), e106010 (2021)
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56.
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Pein, F.; Eltzner, B.; Munk, A.: Analysis of patchclamp recordings: model-free multiscale methods and software. European Biophysics Journal 50 (2), S. 187 - 209 (2021)
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57.
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Risselada, H. J.; Grubmüller, H.: How proteins open fusion pores: insights from molecular simulations. European Biophysics Journal 50 (2), S. 279 - 293 (2021)
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58.
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Rivière, G.; Jaipuria, G.; Andreas, L. B.; Leonov, A.; Giller, K.; Becker, S.; Zweckstetter, M.: Membrane-embedded TSPO: an NMR view. European Biophysics Journal 50 (2), S. 173 - 180 (2021)
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59.
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Tkach, I.; Diederichsen, U.; Bennati, M.: Studies of transmembrane peptides by pulse dipolar spectroscopy with semi-rigid TOPP spin labels. European Biophysics Journal 50 (2), S. 143 - 157 (2021)
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60.
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Levien, M.; Reinhard, M.; Hiller, M.; Tkach, I.; Bennati, M.; Orlando, T.: Spin density localization and accessibility in organic radicals for liquid-state DNP efficiency. Physical Chemistry Chemical Physics 23 (8), S. 4480 - 4485 (2021)
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61.
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Jiang, H.; Tao, X.; Kammler, M.; Ding, F.; Wodtke, A.; Kandratsenka, A.; Miller III, T. F.; Bünermann, O.: Small nuclear quantum effects in scattering of H and D from graphene. Journal of Physical Chemistry Letters 12 (7), S. 1991 - 1996 (2021)
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62.
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Liu, H.; Koros, C.; Strohäker, T.; Schulte, C.; Bozi, M.; Varvaresos, S.; de Opakua, A. I.; Simitsi, A. M.; Bougea, A.; Voumvourakis, K. et al.; Maniati, M.; Papageorgiou, S. G.; Hauser, A.‐.; Becker, S.; Zweckstetter, M.; Stefanis, L.; Gasser, T.: A novel SNCA A30G mutation causes familial Parkinsonʼs disease. Movement Disorders, In Press (2021)
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63.
Zeitschriftenartikel
Endres, T.; Solvie, D.; Heidelberger, J. B.; Andriolett, V.; Baluapuri, A.; Ade, C. P.; Muhar, M.; Eilers, U.; Vos, S. M.; Cramer, P. et al.; Zuber, J.; Beli, P.; Popov, N.; Wolf, E.; Gallant, P.; Eilers, M.: Ubiquitylation of MYC couples transcription elongation with double-strand break repair at active promoters. Molecular Cell 81 (4), S. 830 - 844.e13 (2021)
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64.
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Gray, A. L. H.; Steren, C. A.; Haynes, I. W.; Bermejo, G. A.; Favretto, F.; Zweckstetter, M.; Do, T. D.: Structural Flexibility of Cyclosporine A Is Mediated by Amide Cis–Trans Isomerization and the Chameleonic Roles of Calcium. Journal of Physical Chemistry B 125 (5), S. 1378 - 1391 (2021)
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65.
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Sawicka, A.; Villamil, G.; Lidschreiber, M.; Darzacq, X.; Dugast‐Darzacq, C.; Schwalb, B.; Cramer, P.: Transcription activation depends on the length of the RNA polymerase II C‐terminal domain. EMBO Journal In Press, e107015 (2021)
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66.
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Scheffler, K.; Uraji, J.; Jentoft, I.; Cavazza, T.; Mönnich, E.; Mogessie, B.; Schuh, M.: Two mechanisms drive pronuclear migration in mouse zygotes. Nature Communications 12, 841 (2021)
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67.
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Zhang, Y.; Laurentiis, E. D.; Bohnsack, K. E.; Wahlig, M.; Ranjan, N.; Gruseck, S.; Hackert, P.; Wölfle, T.; Rodnina, M. V.; Schwappach, B. et al.; Rospert, S.: Ribosome-bound Get4/5 facilitates the capture of tail-anchored proteins by Sgt2 in yeast. Nature Communications 12, 782 (2021)
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68.
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Tegunov, D.; Xue, L.; Dienemann, C.; Cramer, P.; Mahamid, J.: Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells. Nature Methods 18 (2), S. 186 - 193 (2021)
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69.
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Zheng, X.; Zhang, L.; Kuang, Y.; Venkataramani, V.; Jin, F.; Hein, K.; Zafeiriou, M. P.; Lenz, C.; Moebius, W.; Kilic, E. et al.; Hermann, D. M.; Weber, M. S.; Urlaub, H.; Zimmermann, W.-H.; Bähr, M.; Doeppner, T. R.: Extracellular vesicles derived from neural progenitor cells: A preclinical evaluation for stroke treatment in mice. Translational Stroke Research 12 (1), S. 185 - 203 (2021)
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70.
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Valpadashi, A.; Callegari, S.; Linden, A.; Neumann, P.; Ficner, R.; Urlaub, H.; Deckers, M.; Rehling, P.: Defining the architecture of the human TIM22 complex by chemical crosslinking. FEBS Letters 595 (2), S. 157 - 168 (2021)
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71.
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Downes, D. J.; Beagrie, R. A.; Gosden, M. E.; Telenius, J.; Carpenter, S. J.; Nussbaum, L.; Ornellas, S. D.; Sergeant, M.; Eijsbouts, C. Q.; Schwessinger, R. et al.; Kerry, J.; Roberts, N.; Shivalingam, A.; El-Sagheer, A.; Oudelaar, A. M.; Brown, T.; Buckle, V. J.; Davies, J. O. J.; Hughes, J. R.: High-resolution targeted 3C interrogation of cis-regulatory element organization at genome-wide scale. Nature Communications 12, 531(2021) (2021)
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72.
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Lau, J. A.; Chen, L.; Choudhury, A.; Schwarzer, D.; Verma, V. B.; Wodtke, A. M.: Transporting and concentrating vibrational energy to promote isomerization. Nature 589 (7842), S. 391 - 395 (2021)
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73.
Zeitschriftenartikel
Sieger, A.; Rankovic, M.; Favretto, F.; Ukmar‐Godec, T.; Strohäker, T.; Becker, S.; Zweckstetter, M.: Interplay between tau and α‐synuclein liquid–liquid phase separation. Protein Science, In Press (2021)
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74.
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Thomas, C.; Cavazza, T.; Schuh, M.: Aneuploidy in human eggs: contributions of the meiotic spindle. Biochemical Society Transactions 49 (1), S. 107 - 118 (2021)
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75.
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Zhang, S.; Aibara, S.; Vos, S. M.; Agafonov, D.; Lührmann, R.; Cramer, P.: Structure of a transcribing RNA polymerase II–U1 snRNP complex. Science 371 (6526), S. 305 - 309 (2021)
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76.
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Kokic, G.; Hillen, H. S.; Tegunov, D.; Dienemann, C.; Seitz, F.; Schmitzova, J.; Farnung, L.; Siewert, A.; Höbartner, C.; Cramer, P.: Mechanism of SARS-CoV-2 polymerase stalling by remdesivir. Nature Communications 12, 279 (2021)
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