Vögele, M.; Hummer, G.: Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes. The Journal of Physical Chemistry B 25 (33), pp. 8722 - 8732 (2016)

Cossio, P.; Hummer, G.; Szabo, A.: Kinetic Ductility and Force-Spike Resistance of Proteins from Single-Molecule Force Spectroscopy. Biophysical Journal 111 (4), pp. 832 - 840 (2016)

Mehdipour, A. R.; Hummer, G.: Cardiolipin puts the seal on ATP synthase. Proceedings of the National Academy of Sciences of the United States of America 113 (31), pp. 8568 - 8570 (2016)

Leahy, C. T.; Murphy, R. D.; Hummer, G.; Rosta, E.; Buchete, N.-V.: Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. The Journal of Physical Chemistry Letters 7 (14), pp. 2676 - 2682 (2016)

Covino, R.; Ballweg, S.; Stordeur, C.; Michaelis, J. B.; Puth, K.; Wernig, F.; Bahrami, A. H.; Ernst, A. M.; Hummer, G.; Ernst, R.: A Eukaryotic Sensor for Membrane Lipid Saturation. Molecular Cell 63 (1), pp. 49 - 59 (2016)

Hummer, G.; Wikström, M.: Molecular simulation and modeling of complex I. Biochimica et Biophysica Acta, Bioenergetics 1857 (7), pp. 915 - 921 (2016)

Sugawa, M.; Okazaki, K.-i.; Kobayashi, M.; Matsui, T.; Hummer, G.; Masaike, T.; Nishizaka, T.: F₁-ATPase conformational cycle from simultaneous single-molecule FRET and rotation measurements. Proceedings of the National Academy of Sciences of the United States of America 113 (21), pp. E2916 - E2924 (2016)

Best, R.; Hummer, G.: Microscopic interpretation of folding ϕ-values using the transition path ensemble. Proceedings of the National Academy of Sciences of the United States of America 113 (12), pp. 3263 - 3268 (2016)

Hummer, G.; Köfinger, J.: Bayesian ensemble refinement by replica simulations and reweighting. The Journal of Chemical Physics 143 (24), pp. 243150-1 - 243150-14 (2015)

Vögele, M.; Holm, C.; Smiatek, J.: Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium). The Journal of Chemical Physics 143, pp. 243151-1 - 243151-8 (2015)

Blees, A.; Reichel, K.; Trowitzsch, S.; Fisette, O.; Bock, C.; Abele, R.; Hummer, G.; Schäfer, L. V.; Tampé, R.: Assembly of the MHC I peptideloading complex determined by a conserved ionic lock-switch. Scientific Reports 5, 17341 (2015)

Cossio, P.; Hummer, G.; Szabo, A.: On artifacts in single-molecule force spectroscopy. Proceedings of the National Academy of Sciences of the United States of America 112 (46), pp. 14248 - 14253 (2015)

Barends, T. R.M.; Foucar, L.; Ardevol, A.; Nass, K.; Aquila, A.; Botha, S.; Doak, R. B.; Falahati, K.; Hartmann, E.; Hilpert, M. et al.; Heinz, M.; Hoffmann, M. C.; Köfinger, J.; Koglin, J. E.; Kovacsova, G.; Liang, M.; Milathianaki, D.; Lemke, H. T.; Reinstein, J.; Roome, C. M.; Shoeman, R. L.; Williams, G. J.; Burghardt, I.; Hummer, G.; Boutet, S.; Schlichting, I.: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 350 (6259), pp. 445 - 450 (2015)

Mantsyzov, A. B.; Shen, Y.; Lee, J. H.; Hummer, G.; Bax, A.: MERA: a webserver for evaluating backbone torsion angle distributions in dynamic and disordered proteins from NMR data. Journal of Biomolecular NMR 63 (1), pp. 85 - 95 (2015)

Okazaki, K.-i.; Hummer, G.: Elasticity, friction, and pathway of γ-subunit rotation in F_oF₁-ATP synthase. Proceedings of the National Academy of Sciences of the United States of America 112 (34), pp. 10720 - 10725 (2015)

Hummer, G.; Szabo, A.: Optimal Dimensionality Reduction of Multistate Kinetic and Markov-State Models. The Journal of Physical Chemistry B 119 (29), pp. 9029 - 9037 (2015)

Sali, A.; Berman, H. M.; Schwede, T.; Trewhella, J.; Kleywegt, G.; Burley, S. K.; Markley, J.; Nakamura, H.; Adams, P.; Bonvin, A. M.J.J. et al.; Chiu, W.; Dal Peraro, M.; Di Maio, F.; Ferrin, T. E.; Grünewald, K.; Gutmanas, A.; Henderson, R.; Hummer, G.; Iwasaki, K.; Johnson, G.; Lawson, C. L.; Meiler, J.; Marti-Renom, M. A.; Montelione, G. T.; Nilges, M.; Nussinov, R.; Patwardhan, A.; Rappsilber, J.; Read, R. J.; Saibil, H.; Schröder, G. F.; Schwieters, C. D.; Seidel, C. A.M.; Svergun, D.; Topf, M.; Ulrich, E. L.; Velankar, S.; Westbrook, J. D.: Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23 (7), pp. 1156 - 1167 (2015)

Craveur, P.; Joseph, A. P.; Esque, J.; Narwani, T. J.; Noël, F.; Shinada, N.; Goguet, M.; Leonard, S.; Poulain, P.; Bertrand, O. et al.; Faure, G.; Rebehmed, J.; Ghozlane, A.; Swapna, L. S.; Bhaskara, R.; Barnoud, J.; Téletchéa, S.; Jallu, V.; Cerny, J.; Schneider, B.; Etchebest, C.; Srinivasan, N.; Gelly, J.-C.; de Brevern, A. G.: Protein flexibility in the light of structural alphabets. Frontiers in Molecular Biosciences 2, 20 (2015)

Kmita, K.; Wirth, C.; Warnau, J.; Guerrero-Castillo, S.; Hunte, C.; Hummer, G.; Kaila, V. R.I.; Zwicker, K.; Brandt, U.; Zickermann, V.: Accessory NUMM (NDUFS6) subunit harbors a Zn-binding site and is essential for biogenesis of mitochondrial complex I. Proceedings of the National Academy of Sciences of the United States of America 112 (18), pp. 5685 - 5690 (2015)

Köfinger, J.; Ragusa, M. J.; Lee, I.-H.; Hummer, G.; Hurley, J. H.: Solution Structure of the Atg1 Complex: Implications for the Architecture of the Phagophore Assembly Site. Structure 23 (5), pp. 809 - 818 (2015)

Wikström, M.; Sharma, V.; Kaila, V. R.I.; Hosler, J. P.; Hummer, G.: New Perspectives on Proton Pumping in Cellular Respiration. Chemical Reviews 115 (5), pp. 2045 - 2222 (2015)

Gamiz-Hernandez, A. P.; Magomedov, A.; Hummer, G.; Kaila, V. R.I.: Linear Energy Relationships in Ground State Proton Transfer and Excited State Proton-Coupled Electron Transfer. The Journal of Physical Chemistry B 119 (6), pp. 2611 - 2619 (2015)

Rosta, E.; Hummer, G.: Free Energies from Dynamic Weighted Histogram Analysis Using Unbiased Markov State Model. Journal of Chemical Theory and Computation 11 (1), pp. 276 - 285 (2015)

Nedialkova, L. V.; Amat, M. A.; Kevrekidis, I. G.; Hummer, G.: Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions. The Journal of Chemical Physics 141 (11), pp. 114102 - 114117 (2014)

Hummer, G.: Potassium ions line up. Do K⁺ ions move in single file through potassium channels? Science Magazine 346 (6207), p. 303 - 303 (2014)

Johnson, M. E.; Hummer, G.: Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems. Physical Review X 4 (3), pp. 031037 - 031058 (2014)

Mantsyzov, A. B.; Maltsev, A. S.; Ying, J.; Shen, Y.; Hummer, G.; Bax, A.: A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein. Protein Science 23 (9), pp. 1275 - 1290 (2014)

Kaila, V. R.I.; Wikström, M.; Hummer, G.: Electrostatics, hydration, and proton transfer dynamics in the membrane domain of respiratory complex I. Proceedings of the National Academy of Sciences of the United States of America 111 (19), pp. 6988 - 6993 (2014)

Kaila, V. R.I.; Schotte, F.; Cho, H. S.; Hummer, G.; Anfinrud, P. A.: Contradictions in X-ray structures of intermediates in the photocycle of photoactive yellow protein. Nature Chemistry 6 (4), pp. 258 - 259 (2014)

Rosta, E.; Yang, W.; Hummer, G.: Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis. Journal of the American Chemical Society 136 (8), pp. 3137 - 3144 (2014)

Ceballos, J. A.; Giraldo, M. A.; Cossio, P.: Effects of a disulfide bridge prior to amyloid formation of the ABRI peptide. RSC Advances 4, pp. 36923 - 36928 (2014)

Hummer, G.; Dellago, C.: Computing Equilibrium Free Energies Using Non-Equilibrium Molecular Dynamics. Entropy 16 (1), pp. 41 - 61 (2014)

Cossio, P.; Hummer, G.: Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies. Journal of Structural Biology 184 (3), pp. 427 - 437 (2013)

Best, R. B.; Hummer, G.; Eaton, W. A.: Native contacts determine protein folding mechanisms in atomistic simulations. Proceedings of the National Academy of Sciences of the United States of America 110 (44), pp. 17874 - 17879 (2013)

Okazaki, K.-i.; Hummer, G.: Phosphate release coupled to rotary motion of F₁-ATPase. Proceedings of the National Academy of Sciences of the United States of America 110 (41), pp. 16468 - 16473 (2013)

Ochoa, R.; Soler, M. A.; Gladich, I.; Battisti, A.; Minovski, N.; Rodriguez, A.; Fortuna, S.; Cossio, P.; Laio, A.: Computational Evolution Protocol for Peptide Design. In: Methods in Molecular Biology (MIMB), Vol. 2405, pp. 335 - 359. Humana Press (2022)

Köfinger, J.; Rózycki, B.; Hummer, G.: Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods. In: Methods in Molecular Biology, Vol. 2022, pp. 341 - 352. Springer (2019)

Ochoa, R.; Laio, A.; Cossio, P.: Computational Design of Peptides Bound to the Major Histocompatibility Complex Class II. 64th Annual Meeting of the Biophysical-Society, San Diego, CA, February 15, 2020 - February 19, 2020. Biophysical Journal 118 (3), Supplement 1 Ed., p. 359A (2020)

Karathanasis, C.; Baldering, T. N.; Boeger, C.; Harwardt, M.-L. I. E.; Li, Y.; Schroeder, M. S.; Deussner-Helfmann, N. S.; Glaesmann, M.; Malkusch, S.; Dietz, M. S. et al.; Hafner, A.-S.; Schuman, E.; Hummer, G.; Heilemann, M.: Quantitative single-molecule localization microscopy reports on protein numbers in signaling protein complexes. In: Proceedings of SPIE: Single molecule spectroscopy and superresolution imaging XIII, Vol. 11246, UNSP 112460N (Eds. Gregor, I.; Koberling, F.; Erdmann, R.). SPIE BIOS, San Francisco, Carlifornia, United States, February 01, 2020 - February 02, 2020. Spie-Int Soc Optical Engineering, Bellingham (2020)

Krüger, C.; Fricke, F.; Karathanasis, C.; Dietz, M. S.; Malkusch, S.; Hummer, G.; Heilemann, M.: Molecular counting of membrane receptor subunits with single-molecule localization microscopy. In: Proceedings SPIE 10071, Single Molecule Spectroscopy and Superresolution Imaging X, Vol. 10071, 100710K. SPIE BiOS, 2017, San Francisco, California, United States, January 28, 2017 - February 02, 2017. (2017)

von Bülow, S.: Molecular Simulations Towards Cell-Scale Processes. Dissertation, 197 pp., Fachbereich Physik, Johann Wolfgang Goethe Universität, Frankfurt am Main (2022)

Cruz-León, S.: Metal Cations and Nucleic Acids: Accurate Force Fields and Atomistic Insights from Molecular Dynamics Simulations. Dissertation, 116 pp., Fachbereich Biochemie, Chemie und Pharmazie, Johann Wolfgang Goethe Universität, Frankfurt am Main (2022)

Siggel, M.: Shaping and Remodeling of Biological Membranes. Dissertation, 180 pp., Fachbereich Physik, Johann Wolfgang Goethe Universität, Frankfurt am Main (2021)

Heinz, M.: Molecular Simulation and Modeling of Chemically Modified Nucleic Acids. Dissertation, 174 pp., Fachbereich Biochemie, Chemie und Pharmazie, Johann Wolfgang Goethe Universität, Frankfurt am Main (2021)

Linke, M.: Methods for Simulation and Calculation of Diffusion. Dissertation, 162 pp., Fachbereich Physik, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2020)

Warnau, J.: Computational Studies of Membrane-bound Proteins Na⁺/H⁺-Antiporter and Respiratory Complex I. Dissertation, 97 pp., Fakultät für Chemie, Technische Universität München, Garching bei München (2019)

Vögele, M.: Theory and Simulation of Diffusion and Self-Assembly in Lipid Membranes. Dissertation, 242 pp., Fachbereich 13 (Physik), Goethe-Universität Frankfurt, Frankfurt am Main (2019)

Reichel, K.: Computational Modeling of Membrane Proteins with Sparse Experimental Data. Dissertation, 179 pp., Fachbereich Biochemie, Chemie, Pharmazie, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2017)

Mehdipour, A. R.: Computational study of transport mechanism in LeuT fold transporters. Dissertation, 187 pp., Fachbereich Biochemie, Chemie und Pharmazie, Goethe Universität, Frankfurt am Main (2015)

Köfinger, J.: Integration of experimental data and molecular simulations. Habilitation, 79 pp., Fachbereich Physik, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2022)

Gemeinhardt, T. M.: Transport mechanism of the SLC23 transporter family. Master, 114 pp., Fachbereich 14 (Biochemie, Chemie, Pharmazie), Goethe-Universität Frankfurt, Frankfurt am Main (2019)

Jung, H.: Automatically discovering molecular reaction mechanisms. Master, 96 pp., Fachbereich Physik, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2019)

Quoika, P.: Thermodynamic and structural properties of dense protein solutions. Master, 145 pp., Fachbereich Physik, Goethe-Universität Frankfurt, Frankfurt am Main (2018)

Schulz, L.: Lead discovery from the mycobacterial ATP synthase Fo rotor ring and characterisation of its binding site. Master, 75 pp., Goethe-Universität Frankfurt, Frankfurt am Main (2017)

Grotz, K. K.: Conformational Dynamics of Single-Stranded Nucleic Acids - A Comparison of Molecular Dynamics Simulations to Single-Molecule FRET Experiments. Master, 102 pp., Goethe-Universität Frankfurt, Fachbereich Physik, Frankfurt am Main (2017)

Linker, S. M.: Predicting Drug-Fragment Binding Sites with Molecular Dynamics Simulations and Markov State Models. Master, 97 pp., Goethe-Universität Frankfurt, Frankfurt am Main (2017)

Gecht, M.: Biophysical analysis of a membrane sensing amphipathic helix in vitro and in silico. Master, 89 pp., Fachbereich Biochemie, Chemie, Pharmazie, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2017)

Heinz, M.: Protein Ligand Dynamics in Myoglobin. Master, 66 pp., Institut für Physikalische und Theoretische Chemie, Goethe-Universität Frankfurt, Frankfurt am Main (2015)

Jost-Lopez, A.: Coarse-Grained Molecular Simulations of Weak Protein Complexes. Master, 66 pp., Goethe Universität, Frankfurt (2014)

Sadowski, S.: How CHMP1b interacts with the membrane. Bachelor, 54 pp., Fachbereich Physik, Johann Wolfgang Goethe-Universität, Frankfurt am Main (2021)

Roy, S.: Integrating experimental data into replica simulations of biomolecules. Bachelor, 96 pp., Goethe-Universität, Frankfurt am Main (2018)

Jung, H.: „Shooting from the top“: Transition path sampling of paths with variable length. Bachelor, 45 pp., Fachbereich Biophysik, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main (2015)