Publikationen Gerhard Hummer

Zeitschriftenartikel (382)

2025
Zeitschriftenartikel
Rosenkranz, N.; Birtasu, A. N.; Wieland, K.; Rehm, L.; Sharma, R.; Vats, A.; Manger, S.; Srivastava, A.; Bhattacharya, A.; Hummer, G. et al.; Frangakis, A. S.; Gottschalk, A.: In situ structure of a gap junction-stomatin complex. Science Advances 11 (45), eaea8596 (2025)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Yang, T.-J.; Mukherjee, S.; Langer, J. D.; Hummer, G.; McDowell, M. A.: SND3 is the membrane insertase within a distinct SEC61 translocon complex. Nature Communications 16, 9566 (2025)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Hasselbeck, S.; Wang, J.; Bai, Z.; Hüfner, T.; Hummer, G.; Grote, P.; Cheng, X.: A Chemically Induced CRISPR/dCas13FCPF Platform for Precise and Programmable RNA Regulation. Journal of Medicinal Chemistry (2025)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Majtner, T.; Kreysing, J. P.; Tuijtel, M.; Cruz-León, S.; Liu, J.; Hummer, G.; Beck, M.; Turoňová, B.: cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography. Communications Biology 8, 1443 (2025)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Ho-Xuan, H.; Bruckmann, A.; Natali, L.; Prieto-Garcia, C.; Stuke, J. F. M.; Brunello, L.; Vicente, A.; Pfab, A.; Wesseling, H.; Cano-Franco, S. et al.; Khatri, A.; Larivera, S.; Sanz-Martinez, P.; de la Cruz-Thea, B.; Jacomin, A.-C.; Prochazka, J.; Feederle, R.; Dötsch, V.; Sedlacek, R.; Hummer, G.; Kaiser, S.; Dikic, I.; Musri, M. M.; Meister, G.; Stolz, A.: YTHDF proteins and m6A-RNA clients undergo autophagic turnover during contact inhibition. Cell Reports 44 (9), 116188 (2025)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Fábián, B.; Stuke, J. F. M.; Heinz, M.; Hummer, G.: AlphaFold modeling of polyubiquitin complexes and covalently linked proteins. Cell Reports Physical Science 6 (9), 102796 (2025)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Horvath, F.; Jung, H.; Grabmayr, H.; Fahrner, M.; Romanin, C.; Hummer, G.: STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling. Proceedings of the National Academy of Sciences of the United States of America 122 (35), e2506516122 (2025)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Adriaenssens, E.; Schaar, S.; Cook, A. S. I.; Stuke, J. F. M.; Sawa-Makarska, J.; Nguyen, T. N.; Ren, X.; Schuschnig, M.; Romanov, J.; Khuu, G. et al.; Uoselis, L.; Lazarou, M.; Hummer, G.; Hurley, J. H.; Martens, S.: Reconstitution of BNIP3/NIX-mitophagy initiation reveals hierarchical flexibility of the autophagy machinery. Nature Cell Biology 27 (8), S. 1272 - 1287 (2025)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Stuke, J. F. M.; Hummer, G.: AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy. Autophagy 21 (10), S. 2192 - 2212 (2025)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Zeitschriftenartikel
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 22 (4), S. 641 - 645 (2025)
MPG.PuRe
DOI
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
pre-print
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)
MPG.PuRe
DOI
Full
2024
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Zeitschriftenartikel
Köfinger, J.; Hummer, G.: Encoding prior knowledge in ensemble refinement. The Journal of Chemical Physics 160, 114111 (2024)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Blanc, F. E. C.; Hummer, G.: Mechanism of proton-powered c-ring rotation in a mitochondrial ATP synthase. PNAS 121 (11), e2314199121 (2024)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
2023
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Zeitschriftenartikel
Bullerjahn, J. T.; Fábián, B.; Hummer, G.: Efficient generation of random rotation matrices in four dimensions. Physical Review E 108 (3), 035307 (2023)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
2022
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)
MPG.PuRe
DOI
Full
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
Zeitschriftenartikel
Schaefer, S. L.; Hummer, G.: Sublytic gasdermin-D pores captured in atomistic molecular simulations. eLife 11, e81432 (2022)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
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)
MPG.PuRe
DOI
publisher-version
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
Full
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)
MPG.PuRe
DOI
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)
MPG.PuRe
DOI
Full
2021
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
DOI
Full
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
DOI
Full
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
DOI
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
DOI
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
DOI
Full
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
DOI
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
DOI
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
DOI
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
DOI
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
DOI
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
DOI
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
DOI
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
DOI
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
DOI
Full
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
DOI
Full
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
DOI
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
DOI
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
DOI
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
DOI
2020
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
DOI
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
DOI
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
DOI
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
DOI
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
DOI
Full
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
DOI
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
DOI
Full
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
DOI
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
DOI
Web-Ansicht
Seite Drucken
Im neuen Fenster öffnen
Geschätzte DIN-A4 Seiten-Breite
Zur Redakteursansicht