Max-Planck-Institut für Biophysik

Publikationen von Gerhard Hummer

Alle Typen

Zeitschriftenartikel (374)

1.

Zeitschriftenartikel

Stautz, J.; Griwatz, D.; Kaltwasser, S.; Mehdipour, A. R.; Ketter, S.; Thiel, C.; Wunnicke, D.; Schrecker, M.; Mills, D. J.; Hummer, G. et al.; Vonck, J.; Hänelt, I.: A short intrinsically disordered region at KtrB’s N-terminus facilitates allosteric regulation of K⁺ channel KtrAB. Nature Communications 16, 4252 (2025)

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2.

Zeitschriftenartikel

Stuke, J. F. M.; Hummer, G.: AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy. Autophagy (2025)

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3.

Zeitschriftenartikel

Cook, A. S. I.; Chen, M.; Nguyen, T. N.; Cabezudo, A. C.; Khuu, G.; Rao, S.; Garcia, S. N.; Yang, M.; Iavarone, A. T.; Ren, X. et al.; Lazarou, M.; Hummer, G.; Hurley, J. H.: Structural pathway for PI3-kinase regulation by VPS15 in autophagy. Science 388 (6743), eadl3787 (2025)

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4.

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Amaro, R. E.; Åqvist, J.; Bahar, I.; Battistini, F.; Bellaiche, A.; Beltran, D.; Biggin, P. C.; Bonomi, M.; Bowman, G. R.; Bryce, R. A. et al.; Bussi, G.; Carloni, P.; Case, D. A.; Cavalli, A.; Chang, C.-E. A.; Cheatham, T. E.; Cheung, M. S.; Chipot, C.; Chong, L. T.; Choudhary, P.; Cisneros, G. A.; Clementi, C.; Collepardo-Guevara, R.; Coveney, P.; Covino, R.; Crawford, T. D.; Dal Peraro, M.; de Groot, B. L.; Delemotte, L.; De Vivo, M.; Essex, J. W.; Fraternali, F.; Gao, J.; Gelpí, J. L.; Gervasio, F. L.; González-Nilo, F. D.; Grubmüller, H.; Guenza, M. G.; Guzman, H. V.; Harris, S.; Head-Gordon, T.; Hernandez, R.; Hospital, A.; Huang, N.; Huang, X.; Hummer, G.; Hummer, G.; Iglesias-Fernández, J.; Jensen, J. H.; Jha, S.; Jiao, W.; Jorgensen, W. L.; Kamerlin, S. C. L.; Khalid, S.; Laughton, C.; Levitt, M.; Limongelli, V.; Lindahl, E.; Lindorff-Larsen, K.; Loverde, S.; Lundborg, M.; Luo, Y. L.; Luque, F. J.; Lynch, C. I.; MacKerell, A. D.; Magistrato, A.; Marrink, S. J.; Martin, H.; McCammon, J. A.; Merz, K.; Moliner, V.; Mulholland, A. J.; Murad, S.; Naganathan, A. N.; Nangia, S.; Noe, F.; Noy, A.; Oláh, J.; O'Mara, M. L.; Ondrechen, M. J.; Onuchic, J. N.; Onufriev, A.; Osuna, S.; Palermo, G.; Panchenko, A. R.; Pantano, S.; Parish, C.; Parrinello, M.; Perez, A.; Perez-Acle, T.; Perilla, J. R.; Pettitt, B. M.; Pietropaolo, A.; Piquemal, J.-P.; Poma, A. B.; Praprotnik, M.; Ramos, M. J.; Ren, P.; Reuter, N.; Roitberg, A.; Rosta, E.; Rovira, C.; Roux, B.; Rothlisberger, U.; Sanbonmatsu, K. Y.; Schlick, T.; Shaytan, A. K.; Simmerling, C.; Smith, J. C.; Sugita, Y.; Świderek, K.; Taiji, M.; Tao, P.; Tieleman, D. P.; Tikhonova, I. G.; Tirado-Rives, J.; Tuñón, I.; van der Kamp, M. W.; van der Spoel, D.; Velankar, S.; Voth, G. A.; Wade, R.; Warshel, A.; Welborn, V. V.; Wetmore, S. D.; Wheeler, T. J.; Wong, C. F.; Yang, L.-W.; Zacharias, M.; Orozco, M.: The need to implement FAIR principles in biomolecular simulations. Nature Methods (2025)

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5.

Zeitschriftenartikel

Poveda Cuevas, S. A.; Lohachova, K.; Markusic, B.; Dikic, I.; Hummer, G.; Bhaskara, R.: Janus-like behavior of intrinsically disordered regions in reticulophagy. Autophagy 21 (3), S. 681 - 683 (2025)

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6.

Zeitschriftenartikel

Kreysing, J. P.; Heidari, M.; Zila, V.; Cruz-León, S.; Obarska-Kosinska, A.; Laketa, V.; Rohleder, L.; Welsch, S.; Köfinger, J.; Turoňová, B. et al.; Hummer, G.; Kräusslich, H.-G.; Beck, M.: Passage of the HIV capsid cracks the nuclear pore. Cell 188 (4), S. 930 - 943.e21 (2025)

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7.

Zeitschriftenartikel

Kutzner, C.; Miletić, V.; Palacio Rodríguez, K.; Rampp, M.; Hummer, G.; de Groot, B. L.; Grubmüller, H.: Scaling of the GROMACS Molecular Dynamics Code to 65k CPU Cores on an HPC Cluster. Journal of Computational Chemistry 46 (5), e70059 (2025)

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8.

Zeitschriftenartikel

Hoffmann, P. C.; Kim, H.; Obarska-Kosinska, A.; Kreysing, J. P.; Andino-Frydman, E.; Cruz-León, S.; Margiotta, E.; Cernikova, L.; Kosinski, J.; Turoňová, B. et al.; Hummer, G.; Beck, M.: Nuclear pore permeability and fluid flow are modulated by its dilation state. Molecular Cell 85 (3), S. 537 - 554.e11 (2025)

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9.

Zeitschriftenartikel

Yin, M. D.; Lemaire, O. N.; Rosas Jiménez, J. G.; Belhamri, M.; Shevchenko, A.; Hummer, G.; Wagner, T.; Murphy, B. J.: Conformational dynamics of a multienzyme complex in anaerobic carbon fixation. Science 387 (6733), S. 498 - 504 (2025)

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10.

Zeitschriftenartikel

Hayashi, K.; Hummer, G.; Joseph, J. A.; Li, R.; Nagai, T.; Onami, S.; Zhang, F.: A round table at IUPAB Congress in Kyoto 2024: Dreaming the next 50 years in our biophysics. Biophysics and Physicobiology 21 (Supplemental2), e212012 (2025)

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11.

Zeitschriftenartikel

Rosas Jiménez, J. G.; Fábián, B.; Hummer, G.: Faster Sampling in Molecular Dynamics Simulations with TIP3P-F Water. Journal of Chemical Theory and Computation 20 (24), S. 11068 - 11081 (2024)

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12.

Zeitschriftenartikel

Heidari, M.; Sikora, M.; Hummer, G.: Refined Protein-Sugar Interactions in the Martini Force Field. Journal of Chemical Theory and Computation 20 (22), S. 10259 - 10265 (2024)

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13.

Zeitschriftenartikel

Poveda-Cuevas, S. A.; Lohachova, K.; Markusic, B.; Dikic, I.; Hummer, G.; Bhaskara, R. M.: Intrinsically disordered region amplifies membrane remodeling to augment selective ER-phagy. Proceedings of the National Academy of Sciences of the United States of America 121 (44), e2408071121 (2024)

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14.

Zeitschriftenartikel

Vallat, B.; Webb, B. M.; Westbrook, J. D.; Goddard, T. D.; Hanke, C. A.; Graziadei, A.; Peisach, E.; Zalevsky, A.; Sagendorf, J.; Tangmunarunkit, H. et al.; Voinea, S.; Sekharan, M.; Yu, J.; A M J J Bonvin, A.; DiMaio, F.; Hummer, G.; Meiler, J.; Tajkhorshid, E.; Ferrin, T. E.; Lawson, C. L.; Leitner, A.; Rappsilber, J.; Seidel, C. A. M.; Jeffries, C. M.; Burley, S. K.; Hoch, J. C.; Kurisu, G.; Morris, K.; Patwardhan, A.; Velankar, S.; Schwede, T.; Trewhella, J.; Kesselman, C.; Berman, H. M.; Sali, A.: IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. Journal of Molecular Biology 436 (17), 168546 (2024)

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15.

Zeitschriftenartikel

Nüesch, M. F.; Pietrek, L.; Holmstrom, E. D.; Nettels, D.; von Roten, V.; Kronenberg-Tenga, R.; Medalia, O.; Hummer, G.; Schuler, B.: Nanosecond chain dynamics of single-stranded nucleic acids. Nature Communications 15 (1), 6010 (2024)

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16.

Zeitschriftenartikel

Ri, K.; Weng, T.-H.; Claveras Cabezudo, A.; Jösting, W.; Zhang, Y.; Bazzone, A.; Leong, N. C. P.; Welsch, S.; Doty, R. T.; Gursu, G. et al.; Lim, T. J. Y.; Schmidt, S. L.; Abkowitz, J. L.; Hummer, G.; Wu, D.; Nguyen, L. N.; Safarian, S.: Molecular mechanism of choline and ethanolamine transport in humans. Nature 630, S. 501 - 508 (2024)

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17.

Zeitschriftenartikel

Gauger, M.; Heinz, M.; Halbritter, A.-L. J.; Stelzl, L. S.; Erlenbach, N.; Hummer, G.; Sigurdsson, S. T.; Prisner, T.: Structure and internal dynamics of short RNA duplexes determined by a combination of pulsed EPR methods and MD simulations. Angewandte Chemie, International Edition in English 63, e202402498 (2024)

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18.

Zeitschriftenartikel

Wang, J.; Heinz, M.; Han, K.; Shah, V. J.; Hasselbeck, S.; Schwalm, M. P.; Rathore, R.; Hummer, G.; Zhou, J.; Dikic, I. et al.; Cheng, X.: Thalidomide derivatives degrade BCL-2 by reprogramming the binding surface of CRBN. Cell Reports Physical Science 5 (5), 101960 (2024)

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19.

Zeitschriftenartikel

Cruz-León, S.; Majtner, T.; Hoffmann, P. C.; Kreysing, J. P.; Kehl, S.; Tuijtel, M.; Schaefer, S. L.; Geißler, K.; Beck, M.; Turoňová, B. et al.; Hummer, G.: High-confidence 3D template matching for cryo-electron tomography. Nature Communications 15, 3992 (2024)

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20.

Zeitschriftenartikel

Tuijtel, M.; Cruz-León, S.; Kreysing, J. P.; Welsch, S.; Hummer, G.; Beck, M.; Turoňová, B.: Thinner is not always better: Optimizing cryo-lamellae for subtomogram averaging. Science Advances 10 (17), eadk6285 (2024)

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21.

Zeitschriftenartikel

Johnson, A. G.; Mayer, M. L.; Schaefer, S. L.; McNamara-Bordewick, N. K.; Hummer, G.; Kranzusch, P. J.: Structure and assembly of a bacterial gasdermin pore. Nature 628 (8008), S. 657 - 663 (2024)

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22.

Zeitschriftenartikel

Köfinger, J.; Hummer, G.: Encoding prior knowledge in ensemble refinement. The Journal of Chemical Physics 160, 114111 (2024)

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23.

Zeitschriftenartikel

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Hierarchical Assembly of Single-Stranded RNA. Journal of Chemical Theory and Computation 20 (5), S. 2246 - 2260 (2024)

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24.

Zeitschriftenartikel

Blanc, F. E. C.; Hummer, G.: Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. PNAS 121 (11), e2314199121 (2024)

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25.

Zeitschriftenartikel

Tsai, Y.-X.; Chang, N.-E.; Reuter, K.; Chang, H.-T.; Yang, T.-J.; von Bülow, S.; Sehrawat, V.; Zerrouki, N.; Tuffery, M.; Gecht, M. et al.; Grothaus, I. L.; Colombi Ciacchi, L.; Wang, Y.-S.; Hsu, M.-F.; Khoo, K.-H.; Hummer, G.; Hsu, S.-T. D.; Hanus, C.; Sikora, M.: Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries. Cell 187 (5), S. 1296 - 1311.e26 (2024)

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26.

Zeitschriftenartikel

Shukla, S.; Chen, W.; Rao, S.; Yang, S.; Ou, C.; Larsen, K. P.; Hummer, G.; Hanson, P. I.; Hurley, J. H.: Mechanism and cellular function of direct membrane binding by the ESCRT and ERES-associated Ca²⁺-sensor ALG-2. Proceedings of the National Academy of Sciences of the United States of America 121 (9), e2318046121 (2024)

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27.

Zeitschriftenartikel

Vögele, M.; Köfinger, J.; Hummer, G.: Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly. ACS applied bio materials 7 (2), S. 528 - 534 (2024)

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28.

Zeitschriftenartikel

Rao, S.; Skulsuppaisarn, M.; Strong, L. M.; Ren, X.; Lazarou, M.; Hurley, J. H.; Hummer, G.: Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore. Science Advances 10 (6), eadj8027 (2024)

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29.

Zeitschriftenartikel

Gewering, T.; Waghray, D.; Parey, K.; Jung, H.; Tran, N. N. B.; Zapata, J.; Zhao, P.; Chen, H.; Januliene, D.; Hummer, G. et al.; Urbatsch, I.; Moeller, A.; Zhang, Q.: Tracing the substrate translocation mechanism in P-glycoprotein. eLife 12, RP90174 (2024)

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30.

Zeitschriftenartikel

Kim, H.; Fábián, B.; Hummer, G.: Neighbor List Artifacts in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 19 (23), S. 8919 - 8929 (2023)

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31.

Zeitschriftenartikel

Pandi, A.; Adam, D.; Zare, A.; Trinh, V. T.; Schaefer, S. L.; Burt, M.; Klabunde, B.; Bobkova, E.; Kushwaha, M.; Foroughijabbari, Y. et al.; Braun, P.; Spahn, C.; Preußer, C.; Pogge von Strandmann, E.; Bode, H. B.; von Buttlar, H.; Bertrams, W.; Jung, A. L.; Abendroth, F.; Schmeck, B.; Hummer, G.; Vázquez, O.; Erb, T. J.: Cell-free biosynthesis combined with deep learning accelerates de novo-development of antimicrobial peptides. Nature Communications 14 (1), 7197 (2023)

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32.

Zeitschriftenartikel

Oosterheert, W.; Blanc, F. E. C.; Roy, A.; Belyy, A.; Sanders, M. B.; Hofnagel, O.; Hummer, G.; Bieling, P.; Raunser, S.: Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nature Structural & Molecular Biology 30 (11), S. 1774 - 1785 (2023)

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33.

Zeitschriftenartikel

Borges-Araújo, L.; Borges-Araújo, A. C.; Ozturk, T. N.; Ramirez-Echemendia, D. P.; Fábián, B.; Carpenter, T. S.; Thallmair, S.; Barnoud, J.; Ingólfsson, H. I.; Hummer, G. et al.; Tieleman, D. P.; Marrink, S. J.; Souza, P. C. T.; Melo, M. N.: Martini 3 Coarse-Grained Force Field for Cholesterol. Journal of Chemical Theory and Computation 19 (20), S. 7387 - 7404 (2023)

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34.

Zeitschriftenartikel

Bullerjahn, J. T.; Fábián, B.; Hummer, G.: Efficient generation of random rotation matrices in four dimensions. Physical Review E 108 (3), 035307 (2023)

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35.

Zeitschriftenartikel

Hanson, S. M.; Scholüke, J.; Liewald, J.; Sharma, R.; Ruse, C.; Engel, M.; Schüler, C.; Klaus, A.; Arghittu, S. M.; Baumbach, F. et al.; Seidenthal, M.; Dill, H.; Hummer, G.; Gottschalk, A.: Structure-function analysis suggests that the photoreceptor LITE-1 is a light-activated ion channel. Current biology: CB 33 (16), S. 3423 - 3435.e5 (2023)

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36.

Zeitschriftenartikel

Wu, D.; Mehdipour, A. R.; Finke, F.; Goojani, H. G.; Groh, R. R.; Grund, T. N.; Reichhart, T. M. B.; Zimmermann, R.; Welsch, S.; Bald, D. et al.; Shepherd, M.; Hummer, G.; Safarian, S.: Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Nature Chemical Biology 19 (8), S. 992 - 1003 (2023)

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37.

Zeitschriftenartikel

Goretzki, B.; Wiedemann, C.; McCray, B. A.; Schäfer, S. L.; Jansen, J.; Tebbe, F.; Mitrovic, S.-A.; Nöth, J.; Cabezudo, A. C.; Donohue, J. K. et al.; Jeffries, C. M.; Steinchen, W.; Stengel, F.; Sumner, C. J.; Hummer, G.; Hellmich, U. A.: Crosstalk between regulatory elements in disordered TRPV4 N-terminus modulates lipid-dependent channel activity. Nature Communications 14, 4165 (2023)

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38.

Zeitschriftenartikel

Bullerjahn, J. T.; von Bülow, S.; Heidari, M.; Hénin, J.; Hummer, G.: Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation 19, S. 3406 - 3417 (2023)

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39.

Zeitschriftenartikel

Foronda, H.; Fu, Y.; Covarrubias-Pinto, A.; Bocker, H. T.; González, A.; Seemann, E.; Franzka, P.; Bock, A.; Bhaskara, R. M.; Liebmann, L. et al.; Hoffmann, M. E.; Katona, I.; Koch, N.; Weis, J.; Kurth, I.; Gleeson, J. G.; Reggiori, F.; Hummer, G.; Kessels, M. M.; Qualmann, B.; Mari, M.; Dikić, I.; Hübner, C. A.: Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy. Nature 618 (7964), S. 402 - 410 (2023)

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40.

Zeitschriftenartikel

González, A.; Covarrubias-Pinto, A.; Bhaskara, R. M.; Glogger, M.; Kuncha, S. K.; Xavier, A.; Seemann, E.; Misra, M.; Hoffmann, M. E.; Bräuning, B. et al.; Balakrishnan, A.; Qualmann, B.; Dötsch, V.; Schulman, B. A.; Kessels, M. M.; Hübner, C. A.; Heilemann, M.; Hummer, G.; Dikić, I.: Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum. Nature 618 (7964), S. 394 - 401 (2023)

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41.

Zeitschriftenartikel

Lettl, C.; Schindele, F.; Mehdipour, A. R.; Steiner, T.; Ring, D.; Brack-Werner, R.; Stecher, B.; Eisenreich, W.; Bilitewski, U.; Hummer, G. et al.; Witschel, M.; Fischer, W.; Haas, R.: Selective killing of the human gastric pathogen Helicobacter pylori by mitochondrial respiratory complex I inhibitors. Cell Chemical Biology 30 (5), S. 499 - 512 (2023)

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42.

Zeitschriftenartikel

Yu, M.; Heidari, M.; Mikhaleva, S.; Tan, P. S.; Mingu, S.; Ruan, H.; Reinkemeier, C. D.; Obarska-Kosinska, A.; Siggel, M.; Beck, M. et al.; Hummer, G.; Lemke, E. A.: Visualizing the disordered nuclear transport machinery in situ. Nature 617 (7959), S. 162 - 169 (2023)

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43.

Zeitschriftenartikel

Jung, H.; Covino, R.; Arjun, A.; Leitold, C.; Dellago, C.; Bolhuis, P. G.; Hummer, G.: Machine-guided path sampling to discover mechanisms of molecular self-organization. Nature Computational Science 3 (4), S. 334 - 345 (2023)

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44.

Zeitschriftenartikel

Fábián, B.; Thallmair, S.; Hummer, G.: Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol. Journal of Chemical Theory and Computation 19 (5), S. 1592 - 1601 (2023)

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45.

Zeitschriftenartikel

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Current Opinion in Structural Biology 78, 102501 (2023)

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46.

Zeitschriftenartikel

von Bülow, S.; Sikora, M.; Blanc, F. E. C.; Covino, R.; Hummer, G.: Antibody accessibility determines location of spike surface mutations in SARS-CoV-2 variants. PLoS Computational Biology 19 (1), e1010822 (2023)

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47.

Zeitschriftenartikel

Zhu, R.; Canena, D.; Sikora, M.; Klausberger, M.; Seferovic, H.; Mehdipour, A. R.; Hain, L.; Laurent, E.; Monteil, V.; Wirnsberger, G. et al.; Wieneke, R.; Tampé, R.; Kienzl, N. F.; Mach, L.; Mirazimi, A.; Oh, Y. J.; Penninger, J. M.; Hummer, G.; Hinterdorfer, P.: Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level. Nature Communications 13 (1), 7926 (2022)

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48.

Zeitschriftenartikel

Jensen, L. E.; Rao, S.; Schuschnig, M.; Cada, A. K.; Martens, S.; Hummer, G.; Hurley, J. H.: Membrane curvature sensing and stabilization by the autophagic LC3 lipidation machinery. Science Advances 8 (50), eadd1436 (2022)

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49.

Zeitschriftenartikel

Linke, M.; Quoika, P. K.; Bramas, B.; Köfinger, J.; Hummer, G.: Complexes++: Efficient and versatile coarse-grained simulations of protein complexes and their dense solutions. The Journal of Chemical Physics 157 (20), 204802 (2022)

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50.

Zeitschriftenartikel

Schaefer, S. L.; Hummer, G.: Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 11, e81432 (2022)

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51.

Zeitschriftenartikel

Siggel, M.; Kehl, S.; Reuter, K.; Köfinger, J.; Hummer, G.: TriMem: A parallelized hybrid Monte Carlo software for efficient simulations of lipid membranes. The Journal of Chemical Physics 157 (17), 174801 (2022)

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52.

Zeitschriftenartikel

Bieber, A.; Capitanio, C.; Erdmann, P. S.; Fiedler, F.; Beck, F.; Lee, C.-W.; Li, D.; Hummer, G.; Schulman, B. A.; Baumeister, W. et al.; Wilfling, F.: In situ structural analysis reveals membrane shape transitions during autophagosome formation. Proceedings of the National Academy of Sciences of the United States of America 119 (39), e2209823119 (2022)

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53.

Zeitschriftenartikel

Khera, R.; Mehdipour, A. R.; Bolla, J. R.; Kahnt, J.; Welsch, S.; Ermler, U.; Münke, C.; Robinson, C. V.; Hummer, G.; Xie, H. et al.; Michel, H.: Cryo-EM structures of pentameric autoinducer-2 exporter from Escherichia coli reveal its transport mechanism. The EMBO Journal 41 (18), e109990 (2022)

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54.

Zeitschriftenartikel

Palacio-Rodriguez, K.; Vroylandt, H.; Stelzl, L. S.; Pietrucci, F.; Hummer, G.; Cossio, P.: Transition Rates and Efficiency of Collective Variables from Time-Dependent Biased Simulations. The Journal of Physical Chemistry Letters 13 (32), S. 7490 - 7496 (2022)

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55.

Zeitschriftenartikel

Sušac, L.; Vuong, M. T.; Thomas, C.; von Bülow, S.; O'Brien-Ball, C.; Santos, A. M.; Fernandes, R. A.; Hummer, G.; Tampé, R.; Davis, S. J.: Structure of a fully assembled tumor-specific T cell receptor ligated by pMHC. Cell 185 (17), S. 3201 - 3213 (2022)

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publisher-version

56.

Zeitschriftenartikel

Bullerjahn, J. T.; Hummer, G.: Reversible bond kinetics from single-molecule force spectroscopy experiments close to equilibrium. Physical Review Research 4 (3), 033097 (2022)

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57.

Zeitschriftenartikel

Fábián, B.; Thallmair, S.; Hummer, G.: Small ionic radii limit time step in Martini 3 molecular dynamics simulations. The Journal of Chemical Physics 157 (3), 034101 (2022)

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58.

Zeitschriftenartikel

Mosalaganti, S.; Obarska-Kosinska, A.; Siggel, M.; Taniguchi, R.; Turoňová, B.; Zimmerli, C. E.; Buczak, K.; Schmidt, F. H.; Margiotta, E.; Mackmull, M.-T. et al.; Hagen, W. J. H.; Hummer, G.; Kosinski, J.; Beck, M.: AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science 376 (6598), eabm9506 (2022)

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59.

Zeitschriftenartikel

Cullati, S. N.; Chaikuad, A.; Chen, J.-S.; Gebel, J.; Tesmer, L.; Zhubi, R.; Navarrete-Perea, J.; Guillen, R. X.; Gygi, S. P.; Hummer, G. et al.; Dötsch, V.; Knapp, S.; Gould, K. L.: Kinase domain autophosphorylation rewires the activity and substrate specificity of CK1 enzymes. Molecular Cell 82 (11), S. 2006 - 2020.e8 (2022)

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60.

Zeitschriftenartikel

Seidel, M.; Becker, A.; Pereira, F.; Landry, J. J. M.; de Azevedo, N. T. D.; Fusco, C. M.; Kaindl, E.; Romanov, N.; Baumbach, J.; Langer, J. D. et al.; Schuman, E. M.; Patil, K. R.; Hummer, G.; Benes, V.; Beck, M.: Co-translational assembly orchestrates competing biogenesis pathways. Nature Communications 13, 1224 (2022)

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61.

Zeitschriftenartikel

Stelzl, L. S.; Pietrek, L. M.; Holla, A.; Oroz, J.; Sikora, M.; Köfinger, J.; Schuler, B.; Zweckstetter, M.; Hummer, G.: Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS Au 2 (3), S. 673 - 686 (2022)

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62.

Zeitschriftenartikel

Lambert, E.; Mehdipour, A. R.; Schmidt, A.; Hummer, G.; Perez, C.: Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nature Communications 13 (1), 1022 (2022)

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63.

Zeitschriftenartikel

Gruijs da Silva, L. A.; Simonetti, F.; Hutten, S.; Riemenschneider, H.; Sternburg, E. L.; Pietrek, L. M.; Gebel, J.; Dötsch, V.; Edbauer, D.; Hummer, G. et al.; Stelzl, L. S.; Dormann, D.: Disease-linked TDP-43 hyperphosphorylation suppresses TDP-43 condensation and aggregation. EMBO Journal 41 (3), e108443 (2022)

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64.

Zeitschriftenartikel

Köfinger, J.; Hummer, G.: Empirical optimization of molecular simulation force fields by Bayesian inference. The European Physical Journal B: Condensend Matter Physics 94 (12), 245 (2021)

MPG.PuRe

65.

Zeitschriftenartikel

Zimmerli, C. E.; Allegretti, M.; Rantos, V.; Goetz, S. K.; Obarska-Kosinska, A.; Zagoriy, I.; Halavatyi, A.; Hummer, G.; Mahamid, J.; Kosinski, J. et al.; Beck, M.: Nuclear pores dilate and constrict in cellulo. Science 374 (6573), eabd9776 (2021)

MPG.PuRe

66.

Zeitschriftenartikel

Sim, S. I.; von Bülow, S.; Hummer, G.; Park, E.: Structural basis of polyamine transport by human ATP13A2 (PARK9). Molecular Cell 81, S. 4635 - 4649 (2021)

MPG.PuRe

67.

Zeitschriftenartikel

Zhao, J.; Xie, H.; Mehdipour, A. R.; Safarian, S.; Ermler, U.; Münke, C.; Thielmann, Y.; Hummer, G.; Ebersberger, I.; Wang, J. et al.; Michel, H.: The structure of the Aquifex aeolicus MATE family multidrug resistance transporter and sequence comparisons suggest the existence of a new subfamily. Proceedings of the National Academy of Sciences of the United States of America 118 (46), e2107335118 (2021)

MPG.PuRe

68.

Zeitschriftenartikel

Klaus, M.; Rossini, E.; Linden, A.; Paithankar, K. S.; Zeug, M.; Ignatova, Z.; Urlaub, H.; Khosla, C.; Köfinger, J.; Hummer, G. et al.; Grininger, M.: Solution Structure and Conformational Flexibility of a Polyketide Synthase Module. JACS Au 1 (12), S. 2162 - 2171 (2021)

MPG.PuRe

69.

Zeitschriftenartikel

Müller, D. J.; Dumitru, A. C.; Lo Giudice, C.; Gaub, H. E.; Hinterdorfer, P.; Hummer, G.; De Yoreo, J. J.; Dufrêne, Y. F.; Alsteens, D.: Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chemical Reviews 121 (19), S. 11701 - 11725 (2021)

MPG.PuRe

70.

Zeitschriftenartikel

Reggio, A.; Buonomo, V.; Berkane, R.; Bhaskara, R.; Tellechea, M.; Peluso, I.; Polishchuk, E.; Di Lorenzo, G.; Cirillov, C.; Esposito, M. et al.; Hussain, A.; Huebner, A. K.; Hübner, C. A.; Settembre, C.; Hummer, G.; Grumati, P.; Stolz, A.: Role of FAM134 paralogues in endoplasmic reticulum remodeling, ER-phagy, and Collagen quality control. EMBO Reports 22 (9), e52289 (2021)

MPG.PuRe

71.

Zeitschriftenartikel

Safarian, S.; Opel-Reading, H. K.; Wu, D.; Mehdipour, A. R.; Hards, K.; Harold, L. H.; Radloff, M.; Stewart, I.; Welsch, S.; Hummer, G. et al.; Cook, G. M.; Krause, K. L.; Michel, H.: The cryo-EM structure of the bd oxidase from M. tuberculosis reveals a unique structural framework and enables rational drug design to combat TB. Nature Communications 12 (1), 5236 (2021)

MPG.PuRe

72.

Zeitschriftenartikel

Väth, K.; Mattes, C.; Reinhard, J.; Covino, R.; Stumpf, H.; Hummer, G.; Ernst, R.: Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1. The Journal of Cell Biology 220 (8), e202011078 (2021)

MPG.PuRe

73.

Zeitschriftenartikel

Mukherjee, R.; Bhattacharya, A.; Bojkova, D.; Mehdipour, A. R.; Shin, D.; Khan, K. S.; Hei-Yin Cheung, H.; Wong, K.-B.; Ng, W.; Cinatl, J. et al.; Geurink, P. P.; van der Heden van Noort, G. J.; Rajalingam, K.; Ciesek, S.; Hummer, G.; Dikic, I.: Famotidine inhibits Toll-like receptor 3-mediated inflammatory signaling in SARS-CoV2 infection. The Journal of Biological Chemistry 297 (2), 100925 (2021)

MPG.PuRe

74.

Zeitschriftenartikel

Schaefer, S. L.; Jung, H.; Hummer, G.: Binding of SARS-CoV-2 Fusion Peptide to Host Endosome and Plasma Membrane. The Journal of Physical Chemistry B 125 (28), S. 7732 - 7741 (2021)

MPG.PuRe

75.

Zeitschriftenartikel

Bullerjahn, J. T.; Hummer, G.: Maximum likelihood estimates of diffusion coefficients from single-particle tracking experiments. The Journal of Chemical Physics 154 (23), 234105 (2021)

MPG.PuRe

76.

Zeitschriftenartikel

Mehdipour, A. R.; Hummer, G.: Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike. Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2100425118 (2021)

MPG.PuRe

77.

Zeitschriftenartikel

Ho, N. T.; Siggel, M.; Camacho, K. V.; Bhaskara, R.; Hicks, J. M.; Yao, Y.-C.; Zhang, Y.; Köfinger, J.; Hummer, G.; Noy, A.: Membrane fusion and drug delivery with carbon nanotube porins. Proceedings of the National Academy of Sciences of the United States of America 118 (19), e2016974118 (2021)

MPG.PuRe

78.

Zeitschriftenartikel

Sikora, M.; von Bülow, S.; Blanc, F. E. C.; Gecht, M.; Covino, R.; Hummer, G.: Computational epitope map of SARS-CoV-2 spike protein. PLoS Computational Biology 17 (4), e1008790 (2021)

MPG.PuRe

79.

Zeitschriftenartikel

Siggel, M.; Bhaskara, R.; Moesser, M. K.; Đikić, I.; Hummer, G.: FAM134B-RHD Protein Clustering Drives Spontaneous Budding of Asymmetric Membranes. The Journal of Physical Chemistry Letters 12 (7), S. 1926 - 1931 (2021)

MPG.PuRe

80.

Zeitschriftenartikel

Benayad, Z.; von Bülow, S.; Stelzl, L. S.; Hummer, G.: Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model. Journal of Chemical Theory and Computation 17 (1), S. 525 - 537 (2021)

MPG.PuRe

81.

Zeitschriftenartikel

Bárcena, M.; Barnes, C. O.; Beck, M.; Bjorkman, P. J.; Canard, B.; Gao, G. F.; Gao, Y.; Hilgenfeld, R.; Hummer, G.; Patwardhan, A. et al.; Santoni, G.; Saphire, E. O.; Schaffitzel, C.; Schendel, S. L.; Smith, J. L.; Thorn, A.; Veesler, D.; Zhang, P.; Zhou, Q.: Structural biology in the fight against COVID-19. Nature Structural and Molecular Biology 28 (1), S. 2 - 7 (2021)

MPG.PuRe

82.

Zeitschriftenartikel

Klionsky, D. J.; Abdel-Aziz, A. K.; Abdelfatah, S.; Hummer, G.; 2295 other, A.: Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition). Autophagy 17 (1), S. 1 - 382 (2021)

MPG.PuRe

83.

Zeitschriftenartikel

Collauto, A.; von Bülow, S.; Gophane, D.; Saha, S.; Stelzl, L. S.; Hummer, G.; Sigurdsson, S. T.; Prisner, T.: Compaction of RNA duplexes in the cell. Angewandte Chemie, International Edition in English 59, S. 23025 - 23029 (2020)

MPG.PuRe

84.

Zeitschriftenartikel

Shin, D.; Mukherjee, R.; Grewe, D.; Bojkova, D.; Baek, K.; Bhattacharya, A.; Schulz, L.; Widera, M.; Mehdipour, A. R.; Tascher, G. et al.; Geurink, P. P.; Wilhelm, A.; van der Heden van Noort, G. J.; Ovaa, H.; Müller, S.; Knobeloch, K.-P.; Rajalingam, K.; Schulman, B.; Cinatl, J.; Hummer, G.; Ciesek, S.; Đikić, I.: Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity. Nature 587 (7835), S. 657 - 662 (2020)

MPG.PuRe

85.

Zeitschriftenartikel

Shin, D.; Bhattacharya, A.; Cheng, Y.-L.; Alonso, M. C.; Mehdipour, A. R.; van der Heden van Noort, G. J.; Ovaa, H.; Hummer, G.; Dikic, I.: Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection. eLife 9 (2020)

MPG.PuRe

86.

Zeitschriftenartikel

Sikora, M.; Ermel, U. H.; Seybold, A.; Kunz, M.; Calloni, G.; Reitz, J.; Vabulas, R. M.; Hummer, G.; Frangakis, A. S.: Desmosome architecture derived from molecular dynamics simulations and cryo-electron tomography. Proceedings of the National Academy of Sciences of the United States of America 117 (44), S. 27132 - 27140 (2020)

MPG.PuRe

87.

Zeitschriftenartikel

Turoňová, B.; Sikora, M.; Schürmann, C.; Hagen, W. J. H.; Welsch, S.; Blanc, F. E. C.; von Bülow, S.; Gecht, M.; Bagola, K.; Hörner, C. et al.; van Zandbergen, G.; Landry, J.; de Azevedo, N. T. D.; Mosalaganti, S.; Schwarz, A.; Covino, R.; Mühlebach, M. D.; Hummer, G.; Krijnse Locker, J.; Beck, M.: In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges. Science 370 (6513), S. 203 - 208 (2020)

MPG.PuRe

88.

Zeitschriftenartikel

Gebel, J.; Tuppi, M.; Chaikuad, A.; Hötte, K.; Schröder, M.; Schulz, L.; Löhr, F.; Gutfreund, N.; Finke, F.; Henrich, E. et al.; Mezhyrova, J.; Lehnert, R.; Pampaloni, F.; Hummer, G.; Stelzer, E. H.K.; Knapp, S.; Dötsch, V.: p63 uses a switch-like mechanism to set the threshold for induction of apoptosis. Nature Chemical Biology 16 (10), S. 1078 - 1086 (2020)

MPG.PuRe

89.

Zeitschriftenartikel

Gecht, M.; Siggel, M.; Linke, M.; Hummer, G.; Köfinger, J.: MDBenchmark: A toolkit to optimize the performance of molecular dynamics simulations. The Journal of Chemical Physics 153 (14), 144105 (2020)

MPG.PuRe

90.

Zeitschriftenartikel

Sawa-Makarska, J.; Baumann, V.; Coudevylle, N.; von Bülow, S.; Nogellova, V.; Abert, C.; Schuschnig, M.; Graef, M.; Hummer, G.; Martens, S.: Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 369 (6508), eaaz7714 (2020)

MPG.PuRe

91.

Zeitschriftenartikel

Ortiz , S.; Stanisic, L.; Rodriguez , B. A.; Rampp, M.; Hummer, G.; Cossio, P.: Validation tests for cryo-EM maps using an independent particle set. Journal of Structural Biology: X 4, 100032 (2020)

MPG.PuRe

92.

Zeitschriftenartikel

Bullerjahn, J. T.; von Bülow, S.; Hummer, G.: Optimal estimates of self-diffusion coefficients from molecular dynamics simulations. The Journal of Chemical Physics 153 (2), 024116 (2020)

MPG.PuRe

93.

Zeitschriftenartikel

von Bülow, S.; Bullerjahn, J. T.; Hummer, G.: Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure. The Journal of Chemical Physics 153 (2), 021101 (2020)

MPG.PuRe

94.

Zeitschriftenartikel

Jost Lopez, A.; Quoika, P. K.; Linke, M.; Hummer, G.; Köfinger, J.: Quantifying Protein-Protein Interactions in Molecular Simulations. The Journal of Physical Chemistry B 124 (23), S. 4673 - 4685 (2020)

MPG.PuRe

95.

Zeitschriftenartikel

Wu, X.; Siggel, M.; Ovchinnikov, S.; Mi, W.; Svetlov, V.; Nudler, E.; Liao, M.; Hummer, G.; Rapoport, T. A.: Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 368 (6489), eaaz2449, S. 385 (2020)

MPG.PuRe

96.

Zeitschriftenartikel

Vögele, M.; Bhaskara, R.; Mulvihill, E.; van Pee, K.; Yildiz, Ö.; Kühlbrandt, W.; Müller, D. J.; Hummer, G.: Reply to Desikan et al.: Micelle formation among various mechanisms of toxin pore formation. Proceedings of the National Academy of Sciences of the United States of America 117 (10), S. 5109 - 5110 (2020)

MPG.PuRe

97.

Zeitschriftenartikel

Ballweg, S.; Sezgin, E.; Doktorova, M.; Covino, R.; Reinhard, J.; Wunnicke, D.; Hänelt, I.; Levental, I.; Hummer, G.; Ernst, R.: Regulation of lipid saturation without sensing membrane fluidity. Nature Communications 11, 756 (2020)

MPG.PuRe

98.

Zeitschriftenartikel

Heinz, M.; Erlenbach, N.; Stelzl, L. S.; Thierolf, G.; Kamble, N. R.; Sigurdsson, S. T. H.; Prisner, T. F.; Hummer, G.: High-resolution EPR distance measurements on RNA and DNA with the non-covalent Ǵ spin label. Nucleic Acids Research 48 (2), S. 924 - 933 (2020)

MPG.PuRe

99.

Zeitschriftenartikel

Warnau, J.; Wöhlert, D.; Okazaki, K.-I.; Yildiz, Ö.; Gamiz-Hernandez, A. P.; Kaila, V. R. I.; Kühlbrandt, W.; Hummer, G.: Ion Binding and Selectivity of the Na⁺/H⁺ Antiporter MjNhaP1 from Experiment and Simulation. The Journal of Physical Chemistry B 124 (2), S. 336 - 344 (2020)

MPG.PuRe

100.

Zeitschriftenartikel

Pietrek, L. M.; Stelzl, L. S.; Hummer, G.: Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 16 (1), S. 725 - 737 (2020)

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