Noé, Frank

Markov models of molecular kinetics: Generation and validation

Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne, M., Held, M., Chodera, J. D., Schütte, C., & Noé, F. (2011) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 1,275

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

Noé, F., Schütte, C., Vanden-Eijnden, E., Reich, L., & Weikl, T. R. (2009) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 820

Markov state models of biomolecular conformational dynamics

Chodera, J. D., & Noé, F. (2014) · Current Opinion in Structural Biology

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 776

Scalable emulation of protein equilibrium ensembles with generative deep learning

Lewis, S., Hempel, T., Jiménez-Luna, J., Gastegger, M., Xie, Y., Foong, A. Y. K., Satorras, V. G., Abdin, O., Veeling, B. S., Zaporozhets, I., et al. (2025) · Science

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 390

Scalable emulation of protein equilibrium ensembles with generative deep learning

Lewis, S., Hempel, T., Jiménez Luna, J., Gastegger, M., Xie, Y., Foong, A. Y. K., García Satorras, V., Abdin, O., Veeling, B. S., Zaporozhets, I., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 349

A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems

Noé, F., & Nüske, F. (2013) · Multiscale Modeling & Simulation

Markov Chains and Monte Carlo MethodsStochastic processes and statistical mechanics

Cited by 327

Variational approach to molecular kinetics

Nüske, F., Keller, B. G., Pérez-Hernández, G., Mey, A. S. J. S., & Noé, F. (2014) · Journal of Chemical Theory and Computation

Advanced Physical and Chemical Molecular InteractionsProtein Structure and Dynamics

Cited by 308

Crystal structure of nucleotide-free dynamin

Faelber, K., Posor, Y., Gao, S., Held, M., Roske, Y., Schulze, D., Haucke, V., Noé, F., & Daumke, O. (2011) · Nature

Cellular transport and secretionProtein Kinase Regulation and GTPase Signaling

Cited by 301

Markov state models based on milestoning

Schütte, C., Noé, F., Lu, J., Sarich, M., & Vanden-Eijnden, E. (2011) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 228

On the Approximation Quality of Markov State Models

Sarich, M., Noé, F., & Schütte, C. (2010) · Multiscale Modeling & Simulation

Markov Chains and Monte Carlo MethodsModel Reduction and Neural Networks

Cited by 182

EMMA: A Software Package for Markov Model Building and Analysis

Senne, M., Trendelkamp-Schroer, B., Mey, A. S. J. S., Schütte, C., & Noé, F. (2012) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 148

Probability distributions of molecular observables computed from Markov models

Noé, F. (2008) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 135

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

Noé, F., Doose, S., Daidone, I., Löllmann, M., Sauer, M., Chodera, J. D., & Smith, J. C. (2011) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsAdvanced Fluorescence Microscopy Techniques

Cited by 116

Structure prediction of alternative protein conformations

Bryant, P., & Noé, F. (2024) · Nature Communications

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 105

Kinetic characterization of the critical step in HIV-1 protease maturation

Sadiq, S. K., Noé, F., & De Fabritiis, G. (2012) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsHIV Research and Treatment

Cited by 102

Complex RNA Folding Kinetics Revealed by Single-Molecule FRET and Hidden Markov Models

Keller, B. G., Kobitski, A., Jäschke, A., Nienhaus, G. U., & Noé, F. (2014) · Journal of the American Chemical Society

RNA and protein synthesis mechanismsDNA and Nucleic Acid Chemistry

Cited by 84

Mechanisms of protein–ligand association and its modulation by protein mutations

Held, M., Metzner, P., Prinz, J.-H., & Noé, F. (2011) · Biophysical Journal

Protein Structure and DynamicsDiffusion and Search Dynamics

Cited by 77

Structure prediction of protein-ligand complexes from sequence information with Umol

Bryant, P., Kelkar, A., Guljas, A., Clementi, C., & Noé, F. (2024) · Nature Communications

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 75

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

Chodera, J. D., Swope, W. C., Noé, F., Prinz, J.-H., Shirts, M. R., & Pande, V. S. (2011) · The Journal of Chemical Physics

Advanced Physical and Chemical Molecular InteractionsProtein Structure and Dynamics

Cited by 71

What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models

Suárez, E., Wiewiora, R. P., Wehmeyer, C., Noé, F., Chodera, J. D., & Zuckerman, D. M. (2020) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 65

Navigating protein landscapes with a machine-learned transferable coarse-grained model

Clementi, C., Charron, N., Musil, F., Guljas, A., Chen, Y., Bonneau, K., Pasos-Trejo, A., Venturin, J., Gusew, D., Zaporozhets, I., et al. (2023) · Nature Chemistry

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 65

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

Suárez, E., Wiewiora, R. P., Wehmeyer, C., Noé, F., Chodera, J. D., & Zuckerman, D. M. (2021) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 65

Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics

Keller, B. G., Prinz, J.-H., & Noé, F. (2012) · Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 59

Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile

Bryant, P., & Noé, F. (2024) · PLOS Computational Biology

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 53