More Noé publications

  • 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. E 76, 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.
    Proteins 59, 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.
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