Publications

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2016

Doerr, S. and Harvey, M. J. and Noé, F. and De Fabritiis, G. (2016) HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. J. Chem. Theory Comput., 12 . pp. 1845-1852.

Nüske, F. and Schneider, R. and Vitalini, F. and Noé, F. (2016) Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems. J. Chem. Phys., 144 . 054105.

Trendelkamp-Schroer, B. and Noé, F. (2016) Efficient estimation of rare-event kinetics. Phys. Rev. X, 6 . 011009.

Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424


2015

Biedermann, J. and Ullrich, A. and Schöneberg, J. and Noé, F. (2015) ReaDDyMM: fast interacting-particle reaction-diffusion simulations using graphical processing units. Biophys. J., 108 . pp. 457-461. ISSN 00063495

Boninsegna, L. and Gobbo, G. and Noé, F. and Clementi, C. (2015) Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps. J. Chem. Theory Comput., 11 . pp. 5947-5960.

Gunkel, M. and Schöneberg, J. and Alkhaldi, W. and Irsen, S. and Noé, F. and Kaupp, U. B. and Al-Amoudi, A. (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure, 23 . pp. 628-638.

Noé, F. (2015) Beating the Millisecond Barrier in Molecular Dynamics Simulations. Biophys J., 108 . pp. 228-229.

Noé, F. (2015) Statistical inefficiency of Markov model count matrices. preprint . (Unpublished)

Noé, F. and Clementi, C. (2015) Kinetic distance and kinetic maps from molecular dynamics simulation. J. Chem. Theory Comput., 11 . pp. 5002-5011.

Plattner, N. and Noé, F. (2015) Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat. Commun., 6 . p. 7653.

Reubold, T. F. and Faelber, K. and Plattner, N. and Posor, Y. and Branz, K. and Curth, U. and Schlegel, J. and Anand, R. and Manstein, D. and Noé, F. and Haucke, V. and Daumke, O. and Eschenburg, S. (2015) Crystal structure of the dynamin tetramer. Nature, 525 . pp. 404-408.

Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 . pp. 5525-5542.

Schror, M. and Mey, A.S.J.S. and Noé, F. and MacPhee, C. (2015) Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models. J. Chem. Phys. Lett., 6 . pp. 1076-1081.

Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 . p. 174101.

Ullrich, A. and Böhme, M. A. and Schöneberg, J. and Depner, H. and Sigrist, S. J. and Noé, F. (2015) Dynamical organization of Syntaxin-1A at the presynaptic active zone. PLoS Comput. Biol., 11 . e1004407.

Vener, M. V. and Odinokov, A. V. and Wehmeyer, C. and Sebastiani, D. (2015) The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. The Journal of Chemical Physics, 142 (21). p. 215106. ISSN 0021-9606

Vitalini, F. and Mey, A.S.J.S. and Noé, F. and Keller, B. (2015) Dynamic Properties of Force Fields. J. Chem. Phys., 142 . 084101.

Vitalini, F. and Noé, F. and Keller, B. (2015) A basis set for peptides for the variational approach to conformational kinetics. J. Chem. Theory Comput., 11 . pp. 3992-4004.

Wu, H. (2015) Maximum Margin Clustering for State Decomposition of Metastable Systems. Neurocomputing, 164 . pp. 5-22. ISSN 0925-2312

Wu, H. and Noé, F. (2015) Gaussian Markov transition models of molecular kinetics. J. Chem. Phys., 142 . 084104.

Wu, H. and Prinz, J.-H. and Noé, F. (2015) Projected Metastable Markov Processes and Their Estimation with Observable Operator Models. J. Chem. Phys., 143 . p. 144101.


2014

Bowman, G. R. and Pande, V. S. and Noé, F., eds. (2014) An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, 797 . Springer.

Bowman, G. R. and Pande, V. S. and Noé, F. (2014) Introduction and overview of this book. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, 797 . Springer, pp. 1-6.

Chodera, J. D. and Noé, F. (2014) Markov state models of biomolecular conformational dynamics. Curr. Opin. Struct. Biol., 25 . pp. 135-144.

Keller, B. and Kobitski, A. and Jäschke, A. and Nienhaus, G.U. and Noé, F. (2014) Complex RNA folding kinetics revealed by single molecule FRET and hidden Markov models. J. Am. Chem. Soc., 136 . pp. 4534-4543.

Mey, A.S.J.S. and Wu, H. and Noé, F. (2014) xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states. Phys. Rev. X, 4 . 041018.

Nüske, F. and Keller, B. and Pérez-Hernández, G. and Mey, A.S.J.S. and Noé, F. (2014) Variational Approach to Molecular Kinetics. J. Chem. Theory Comput., 10 . pp. 1739-1752.

Noé, F. and Chodera, J. D. (2014) Uncertainty Estimation. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, 797 . Springer, pp. 61-74.

Noé, F. and Prinz, J.-H. (2014) Analysis of Markov Models. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, 797 . Springer, pp. 75-90.

Prinz, J.-H. and Chodera, J. D. and Noé, F. (2014) Estimation and Validation of Markov Models. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology , 797 . Springer, pp. 45-60.

Prinz, J.-H. and Chodera, J. D. and Noé, F. (2014) Spectral rate theory for two-state kinetics. Phys Rev X, 4 . 011020.

Schöneberg, J. and Heck, M. and Hofmann, K. P. and Noé, F. (2014) Explicit Spatio-temporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes. Biophys. J., 107 . pp. 1042-1053. ISSN 00063495

Schöneberg, J. and Ullrich, Alexander and Noé, F. (2014) Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophysics, 7 . p. 11.

Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F. (2014) Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. J. Chem. Phys., 141 . p. 214106.

Wu, H. and Noé, F. (2014) Optimal estimation of free energies and stationary densities from multiple biased simulations. SIAM Multiscale Model. Simul., 12 . pp. 25-54.


2013

Faelber, K. and Gao, S. and Held, M. and Posor, Y. and Haucke, V. and Noé, F. and Daumke, O. (2013) Oligomerization of dynamin superfamily proteins in health and disease. In: Progress in Molecular Biology and Translational Science. Elsevier, pp. 411-443.

Lindner, Benjamin and Yi, Zheng and Prinz, J.-H. and Smith, J. C. and Noé, F. (2013) Dynamic Neutron Scattering from Conformational Dynamics I: Theory and Markov models. J. Chem. Phys., 139 . p. 175101.

Noé, F. (2013) Markov Models of Molecular Kinetics. In: Encyclopedia of Biophysics. Springer, pp. 1385-1394.

Noé, F. and Nüske, F. (2013) A variational approach to modeling slow processes in stochastic dynamical systems. SIAM Multiscale Model. Simul., 11 . pp. 635-655.

Noé, F. and Wu, H. and Prinz, J.-H. and Plattner, N. (2013) Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules. J. Chem. Phys., 139 . p. 184114.

Pérez-Hernández, G. and Paul, F. and Giorgino, T. and de Fabritiis, G. and Noé, F. (2013) Identification of slow molecular order parameters for Markov model construction. J. Chem. Phys., 139 . 015102.

Posor, Y. and Eichhorn-Gruenig, M. and Puchkov, D. and Schöneberg, J. and Ullrich, A. and Lampe, A. and Müller, R. and Zarbakhsh, S. and Gulluni, F. and Hirsch, E. and Krauss, M. and Schultz, C. and Schmoranzer, J. and Noé, F. and Haucke, V. (2013) Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature, 499 . pp. 233-237.

Schaller, Christoph (2013) STORMicroscopy: A Mathematical Analysis. Masters thesis, FU Berlin.

Schöneberg, J. and Noé, F. (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLoS ONE, 8 . e74261. ISSN 1932-6203

Steger, Katrin and Bollmann, Stefan and Noé, F. and Doose, S. (2013) Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale. Phys. Chem. Chem. Phys., 15 . pp. 10435-10445.

Trendelkamp-Schroer, B. and Noé, F. (2013) Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution. J. Phys. Chem., 138 . p. 164113.

Yi, Zheng and Lindner, Benjamin and Prinz, J.-H. and Noé, F. and Smith, J. C. (2013) Dynamic Neutron Scattering from Conformational Dynamics II: Application using Molecular Dynamics Simulation and Markov modeling. J. Chem. Phys., 139 . p. 175102.


2012

Faelber, K. and Held, M. and Gao, S. and Posor, Y. and Haucke, V. and Noé, F. and Daumke, O. (2012) Structural insights into dynamin-mediated membrane fission. Structure, 20 . 1621-1628.

Held, M. and Imhof, P. and Keller, B. and Noé, F. (2012) Modulation of a ligand’s energy landscape and kinetics by the chemical environment. J. Phys. Chem. B, 116 . pp. 13597-13607.

Held, M. and Noé, F. (2012) Calculating kinetics and pathways of protein–ligand association. Eur. J. Cell Biol., 91 . pp. 357-364.

Keller, B. and Prinz, J.-H. and Noé, F. (2012) Markov models and dynamical fingerprints: unraveling the complexity of molecular kinetics. Chem. Phys., 396 . pp. 92-107.

Keller, B. and Prinz, J.-H. and Noé, F. (2012) Resolving the apparent gap in complexity between simulated and measured kinetics of biomolecules. From Computational Biophysics to Systems Biology (CBSB11) Proceedings, IAS Series, 8 . pp. 61-64.

Nüske, F. (2012) A variational approach for conformation dynamics. Masters thesis, FU Berlin.

Peuker, Sebastian and Cukkemane, Abhishek and Held, M. and Noé, F. and Kaupp, Benjamin and Seifert, Reinhard (2012) Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys. J., 104 . pp. 63-74.

Prinz, J.-H. (2012) Advanced estimation methods for Markov models of dynamical systems. PhD thesis, FU Berlin.

Sadiq, S. K. and Noé, F. and de Fabritiis, G. (2012) Kinetic characterization of the critical step in HIV-1 protease maturation. Proc. Natl. Acad. Sci. USA, 109 . pp. 20449-20454.

Senne, M. and Trendelkamp-Schroer, B. and Mey, A.S.J.S. and Schütte, Ch. and Noé, F. (2012) EMMA - A software package for Markov model building and analysis. Journal of Chemical Theory and Computation, 8 . pp. 2223-2238.


2011

Chodera, J. D. and Swope, W. D. and Noé, F. and Prinz, J.-H. and Shirts, M. R. and Pande, V. S. (2011) Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures. J. Chem. Phys., 134 (24). p. 244107.

Faelber, Katja and Posor, York and Held, M. and Roske, Yvette and Schulze, Dennis and Haucke, Volker and Noé, F. and Daumke, Oliver (2011) Crystal structure of nucleotide-free dynamin. Nature, 477 . pp. 556-560.

Keller, B. and Hünenberger, Philippe and van Gunsteren, Wilfred (2011) An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. J. Chem. Theo. Comput., 7 . pp. 1032-1044.

Noé, F. and Doose, S. and Daidone, I. and Löllmann, M. and Chodera, J. D. and Sauer, M. and Smith, J. C. (2011) Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc. Natl. Acad. Sci. USA, 108 . pp. 4822-4827.

Prinz, J.-H. and Chodera, J. D. and Pande, V. S. and Swope, W. D. and Smith, J. C. and Noé, F. (2011) Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J. Chem. Phys., 134 (24). p. 244108.

Prinz, J.-H. and Held, M. and Smith, J. C. and Noé, F. (2011) Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes. Multiscale Model. Simul., 9 . pp. 545-567.

Prinz, J.-H. and Keller, B. and Noé, F. (2011) Probing molecular kinetics with Markov models: Metastable states, transition pathways and spectroscopic observables. Phys. Chem. Chem. Phys., 13 . pp. 16912-16927.

Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Senne, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F. (2011) Markov models of molecular kinetics: Generation and Validation. J. Chem. Phys., 134 . p. 174105.

Schütte, Ch. and Noé, F. and Lu, Jianfeng and Sarich, M. and Vanden-Eijnden, E. (2011) Markov State Models Based on Milestoning. J. Chem. Phys., 134 (20). 204105 .

Splettstößer, T. and Holmes, K. C. and Noé, F. and Smith, J. C. (2011) Structural modeling and molecular dynamics simulation of the actin filament. Proteins, 79 . pp. 2033-2043.

Wu, H. and Noé, F. (2011) Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations. Phys. Rev. E, 83 (3). 036705.

Wu, H. and Noé, F. (2011) A flat Dirichlet process switching model for Bayesian estimation of hybrid systems. Procedia Computer Science, 4 . pp. 1393-1402.


2010

Bernhard, S. and Noé, F. (2010) Optimal Identification of Semi-Rigid Domains in Macromolecules from Molecular Dynamics Simulation. PLoS One, 5 . e10491.

Chodera, J. D. and Noé, F. (2010) Probability distributions of molecular observables computed from Markov models. II: Uncertainties in observables and their time-evolution. J. Chem. Phys, 133 (10). p. 105102.

Held, M. and Metzner, Ph. and Prinz, J.-H. and Noé, F. (2010) Mechanisms of Protein-Ligand association and its modulation by protein mutations. Biophys. J., 100 (3). pp. 701-710.

Kavalar, Martin (2010) Conformational Dynamics of a Peptide Ligand in Solvent and in Complex with a MHC-I Protein. Masters thesis, FU Berlin.

Keller, B. and Gattin, Z. and van Gunsteren, W. F. (2010) What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation. PROTEINS: Structure, Function, and Bioinformatics, 78 (7). pp. 1677-1690.

Sarich, M. and Noé, F. and Schütte, Ch. (2010) On the Approximation Quality of Markov State Models. Multiscale Model. Simul., 8 (4). pp. 1154-1177.

Seibert, Johannes (2010) Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolution. Masters thesis, FU Berlin.

Wu, H. and Noé, F. (2010) Maximum a posteriori estimation for Markov chains based on Gaussian Markov random fields. Procedia Computer Science, 1 (1). pp. 1665-1673.

Wu, H. and Noé, F. (2010) Probability Distance Based Compression of Hidden Markov Models. Multiscale Model. Simul., 8 . pp. 1838-1861.


2009

Azhand, Arash (2009) Diffusion Processes with Hidden States from Single Molecule Experiments. Masters thesis, FU Berlin and TU Berlin.

Lüdge, Torsten (2009) A theoretical model of conformational transitions in biomolecules based on single-molecule Förster resonance electron transfer measurements. Masters thesis, FU Berlin and TU Berlin.

Metzner, Ph. and Noé, F. and Schütte, Ch. (2009) Estimating the Sampling Error: Distribution of Transition Matrices and Functions of Transition Matrices for Given Trajectory Data. Phys. Rev. E, 80 (2). 021106.

Noé, F. and Schütte, Ch. and Vanden-Eijnden, E. and Reich, L. and Weikl, T. (2009) Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106 (45). pp. 19011-19016.

Schütte, Ch. and Noé, F. and Meerbach, E. and Metzner, Ph. and Hartmann, C. (2009) Conformation Dynamics. Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), . pp. 297-335.

Splettstößer, T. and Noé, F. and Oda, T. and Smith, J. C. (2009) Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerisation-competent superclosed state. Proteins, 76 . pp. 353-364.


2008

Fischbach, M. (2008) Methods for modeling metastable conformational dynamics from trajectory data. Masters thesis, FU Berlin.

Noé, F. (2008) Probability Distributions of Molecular Observables computed from Markov Models. J. Chem. Phys., 128 . p. 244103.

Noé, F. and Daidone, I. and Smith, J. C. and Di Nola, A. and Amadei, A. (2008) Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J. Phys. Chem. B, 112 . pp. 11155-11163.

Noé, F. and Fischer, S. (2008) Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules. Curr. Opin. Struct. Biol., 18 . pp. 154-162.

Sakalli, I. (2008) Parallelization Strategies for a Brownian Dynamics Algorithm. Other thesis, FU Berlin.


2007

Held, M. (2007) Conformational Studies of UDP-N-Acetyl-Glucosamine in Environments of Increasing Complexity. Masters thesis, FU Berlin.

Horenko, I. and Hartmann, C. and Schütte, Ch. and Noé, F. (2007) Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76 (01). 016706.

Noé, F. and Horenko, I. and Schütte, Ch. and Smith, J. C. (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126 (15). p. 155102.

Noé, F. and Oswald, M. and Reinelt, G. (2007) Optimization in Graphs with Limited Information on the Edge Weights. Operations Research Proceedings 2007. Editors: J. Kalcsics and S. Nickel . pp. 435-440.

Noé, F. and Smith, J. C. (2007) Transition Networks: a unifying theme for molecular simulation and computer science. Mathematical Modeling of Biological Systems I, A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (Eds) . pp. 125-144.

Noé, F. and Smith, J. C. and Schütte, Ch. (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann, NIC Series 36 .


2006

Becker, T. and Fischer, S. and Noé, F. and Tournier, A. and Ullmann, M. and Kurkal, V. and Smith, J. C. (2006) Physical and functional aspects of protein dynamics. Soft Condensed Matter Physics in Molecular and Cell Biology, Poon & Andelman (Eds) .

Imhof, P. and Noé, F. (2006) AM1/d Parameters for Magnesium in Metalloenzymes. J. Chem. Theo. Comput., 2 . pp. 1050-1056.

Noé, F. (2006) Transition Networks: Computational Methods for the Comprehensive Analysis of Complex Rearrangements in Proteins. PhD thesis, University of Heidelberg.

Noé, F. and Krachtus, D. and Smith, J. C. and Fischer, S. (2006) Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. J. Chem. Theo. Comput., 2 . pp. 840-857.

Noé, F. and Oswald, M. and Reinelt, G. and Smith, J. C. and Fischer, S. (2006) Computing Best Transition Pathways in High-Dimensional Dynamical Systems. Multisc. Model. Sim. , 5 . pp. 393-419.


2005

Noé, F. and Ille, F. and Smith, J. C. and Fischer, S. (2005) Automated Computation of Low-Energy Pathways for Complex Rearrangements in Proteins: Application to the conformational switch of Ras p21. Proteins, 59 . pp. 534-544.


2003

Becker, T. and Fischer, S. and Noé, F. and Ullmann, M. and Tournier, A. and Smith, J. C. (2003) Protein Dynamics: Glass Transition and Mechanical Function. Advances in Solid State Physics, 43 . pp. 677-694.

Noé, F. and Schwarzl, S. and Fischer, S. and Smith, J. C. (2003) Computational tools for analysing structural changes in proteins in solution. Applied Bioinformatics, 2 . pp. 11-17.


2002

Noé, F. (2002) The Evolution of Cell Colonies in Volvocacean Algae: Investigation by theoretical analysis and computer simulation. Masters thesis, Cork Institute of Technology, Ireland.