M Gunkel et al. (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure, 23 (4): 628-38
H Wu, F Noé (2015) Gaussian Markov transition models of molecular kinetics. J Chem Phys., 142 (8): 084104
F Vitalini, AS Mey, F Noé, BG Keller (2015) Dynamic properties of force fields. J Chem Phys., 142 (8): 084101
J Biedermann, A Ullrich, J Schöneberg, F Noé (2015) ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units. Biophys J., 108 (3): 457-61
F Noé (2015) Beating the millisecond barrier in molecular dynamics simulations. Biophys J., 108 (2): 228-9
H Wu, AS Mey, E Rosta, F Noé (2014) Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. J Chem Phys., 141 (21): 214106
JH Prinz, JD Chodera, F Noé (2014) Spectral rate theory for two-state kinetics. Phys Rev X., 4 (1): 011020
J Schöneberg, M Heck, KP Hofmann, F Noé (2014) Explicit spatiotemporal simulation of receptor-g protein coupling in rod cell disk membranes. Biophys J., 107 (5): 1042-53
JD Chodera, F Noé (2014) Markov state models of biomolecular conformational dynamics. Curr Opin Struct Biol., 25C: 135-144
F Noé, H Wu, JH Prinz, N Plattner (2014) Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules. J Chem Phys., 139 (18): 184114
GR Bowman, VS Pande, F Noé (eds.), (2014) An introduction to Markov State Models and their application to long timescale molecular simulation. Adv Exp Med Biol., 797
Z Yi, B Lindner, JH Prinz, F Noé, JC Smith (2013) Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling. J Chem Phys., 139 (17): 175102
B Lindner, Z Yi, JH Prinz, JC Smith, F Noé (2013) Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models. J Chem Phys., 139 (17): 175101
Y Posor et al. (2013) Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature, 499 (7457): 233-237
G Pérez-Hernández et al. (2013) Identification of slow molecular order parameters for Markov model construction. J Chem Phys., 139 (1): 015102
K Steger, S Bollmann, F Noé, S Doose (2013) Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale. Phys Chem Chem Phys., 15 (25): 10435-45
K Faelber et al. (2013) Oligomerization of dynamin superfamily proteins in health and disease. Prog Mol Biol Transl Sci., 117: 411-43
B Trendelkamp-Schroer and F Noé (2013) Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution. J Chem Phys., 138 (16): 164113
S Peuker et al. (2013) Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys J., 104 (1): 63-74
SK Sadiq, F Noé, G De Fabritiis (2012) Kinetic characterization of the critical step in HIV-1 protease maturation. Proc Natl Acad Sci USA, 109 (50): 20449-54
K Faelber, M Held, S Gao, Y Posor, V Haucke, F Noé, O Daumke (2012) Structural insights into dynamin-mediated membrane fission. Structure, 20 (10): 1621-8
M Held, P Imhof, BG Keller, F Noé (2012) Modulation of a ligand's energy landscape and kinetics by the chemical environment. J Phys Chem B., 116 (46): 13597-607
M Held, F Noé (2011) Calculating kinetics and pathways for protein-ligand association. Eur J Cell Biol., 91 (4): 357-64
K Faelber, Y Posor, S Gao, M Held, Y Roske, D Schulze, V Haucke, F Noé and O Daumke (2011) Crystal structure of nucleotide-free dynamin. Nature, 477 (7366): 556-60
JH Prinz, B Keller, F Noé (2011) Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables. Phys Chem Chem Phys, 13 (38): 16912-27
JH Prinz, M Held, JC Smith, F Noé (2011) Efficient computation, sensitivity, and error analysis of committor probabilities for complex dynamical processes. Multiscale Model. Simul., 9 (2): 545-67
JH Prinz, JD Chodera, VS Pande, WC Swope, JC Smith, F Noé Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J Chem Phys., 134 (24): 244108
JD Chodera, WC Swope, F Noé, JH Prinz, MR Shirts, VS Pande (2011) Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures. J Chem Phys., 134 (24): 244107
C Schütte, F Noé, J Lu, M Sarich, E Vanden-Eijnden (2011) Markov state models based on milestoning. J Chem Phys., 134 (20): 204105
T Splettstoesser, KC Holmes, F Noé, JC Smith (2011) Structural modeling and molecular dynamics simulation of the actin filament. Proteins, 79 (7): 2033-43
JH Prinz, H Wu, M Sarich, B Keller, M Senne, M Held, JD Chodera, C Schütte, F Noé (2011) Markov models of molecular kinetics: Generation and validation. J Chem Phys., 134 (17): 174105
H Wu, F Noé (2011) Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations. Phys Rev E Stat Nonlin Soft Matter Phys., 83 (3 Pt 2): 036705
F Noé, S Doose, I Daidone, M Löllmann, M Sauer, JD Chodera, JC Smith (2011) Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc Natl Acad Sci USA, 108 (12): 4822-7
M Held, P Metzner, JH Prinz, F Noé (2011) Mechanisms of protein-ligand association and its modulation by protein mutations. Biophys J.100(3): 701-10
JD Chodera, F Noé (2010) Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution. J Chem Phys., 13(10):105102
S Bernhard, F Noé (2010) Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation. PLoS One, 5(5):e10491
M Sarich, F Noé and Ch Schütte (2010) On the approximation quality of Markov state models. Mult. Mod. Sim.8(4):1154-77
F Noé, C Schütte, E Vanden-Eijnden, L Reich, TR Weikl (2009) Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci USA., 106(45):19011-6
P Metzner, F Noé and C Schütte (2009) Estimating the sampling error: distribution of transition matrices and functions of transition matrices for given trajectory data. Phys Rev E, 80(2 Pt 1):021106
T Splettstößer, F Noé, T Oda and JC Smith (2009) Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerisation-competent superclosed state Proteins, 76(2):353-64
C Schütte, F Noé, E Meerbach, P Metzner and C Hartmann (2008) Conformation Dynamics Proceedings of the ICIAM 2007
F Noé (2008) Probability Distributions of Molecular Observables computed from Markov Models J. Chem. Phys., 128(24):244103
F Noé and S Fischer (2008) Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules Curr. Opin. Struct. Biol., 18(2):154-162.
F Noé, M Oswald and G Reinelt (2007) Optimization in Graphs with Limited Information on the Edge Weights In: Operations Research Proceedings 2007. J. Kalcsics and S. Nickel (Eds), 435-440, Springer.
I Horenko, C Hartmann, C Schütte and F Noé (2007) Data-based parameter estimation of generalized Langevin processes Phys. Rev. E76, 016706.
F Noé and JC Smith and C Schütte (2007) A network-based approach to biomolecular dynamics. In: From Computational Biophysics to Systems Biology. U. H. E. Hansmann and J. Meinke and S. Mohanty and O. Zimmermann (Eds), 247-250, John von Neumann Institute for Computing, Juelich.
F Noé, I Horenko, C Schütte and JC Smith (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126(15):155102.
F Noé and JC Smith (2007) Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science. In: Mathematical Modeling of Biological Systems, Volume I. A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (eds). Birkhäuser, Boston, 125-144.
P Imhof, F Noé, S Fischer and JC Smith (2006) Parameters for Magnesium in Metalloenzymes. J. Chem. Theo. Comput.2, 1050-1056.
F Noé, D Krachtus, JC Smith and S Fischer (2006) Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. J. Chem. Theo. Comput.2, 840-857
F Noé, M Oswald, G Reinelt, JC Smith and S Fischer (2006) Computing Best Transition Pathways in High-Dimensional Dynamical Systems Multisc. Model. Sim.5, 393-419.
F Noé (2006) Transition Networks: Computational Methods for the Comprehensive Analysis of Complex Rearrangements in Proteins. Ph.D. thesis, University of Heidelberg.
F Noé, JC Smith and S Fischer (2005) Automated Computation of Low-Energy Pathways for Complex Rearrangements in Proteins: Application to the conformational switch of Ras p21. Proteins59, 534-544.
T Becker, S Fischer, F Noé, AL Tournier, GM Ullmann, V Kurkal and JC Smith (2006) Physical and functional aspects of protein dynamics. In: Soft Condensed Matter Physics in Molecular and Cell Biology, Poon & Andelman (Eds), 225-241, Taylor & Francis.
F Noé, SM Schwarzl, S Fischer and JC Smith (2003) Computational tools for analysing structural changes in proteins in solution. Applied Bioinformatics, 2, 11-17.
T Becker, S Fischer, F Noé, M Ullmann, A Tournier and JC Smith (2003) Protein Dynamics: Glass Transition and Mechanical Function. Advances in Solid State Physics 43. Ed. B. Kramer. Springer-Verlag Heidelberg, 677-694.