Browse by Authors

2024

Schebek, Maximilian and Invernizzi, Michele and Noé, Frank and Rogal, Jutta (2024) Efficient Mapping of Phase Diagrams with Conditional Boltzmann Generators. Preprint arXiv . (Unpublished)

Bryant, Patrick and Noé, Frank (2024) Improved Protein Complex Prediction with AlphaFold-Multimer by Denoising the MSA Profile. PLOS Computational Biology, 20 (7).

Bryant, Patrick and Kelkar, Atharva and Guljas, Andrea and Clementi, Cecilia and Noé, Frank (2024) Structure prediction of protein-ligand complexes from sequence information with Umol. Nature Communications, 15 .

Wu, Hao and Noé, Frank (2024) Reaction coordinate flows for model reduction of molecular kinetics. The Journal of Chemical Physics, 160 (4).

Rentsch, Jakob and Bandstra, Selle and Sezen, Batuhan and Sigrist, Philipp Stephan and Bottanelli, Francesca and Schmerl, Bettina and Shoichet, Sarah and Noé, Frank and Sadeghi, Mohsen and Ewers, Helge (2024) Sub-membrane actin rings compartmentalize the plasma membrane. Journal of Cell Biology (JCB), 223 (4).

2023

Jong-Bolm, Daniëlle de and Sadeghi, Mohsen and Bogaciu, Cristian A. and Bao, Guobin and Klaehn, Gabriele and Hoff, Merle and Mittelmeier, Lucas and Basmanav, F. Buket and Noé, Frank and Rizzoli, Silvio O. (2023) Protein nanobarcodes enable single-step multiplexed fluorescence imaging. PLOS BIOLOGY, 21 (12).

Charron, Nicholas E. and Musil, Felix and Guljas, Andrea and Chen, Yaoyi and Bonneau, Klara and Pasos-Trejo, Aldo S. and Venturin, Jacopo and Gusew, Daria and Zaporozhets, Iryna and Krämer, Andreas and Templeton, Clark and Kelkar, Atharva and Durumeric, Alexander E.P. and Olsson, Simon and Pérez, Adrià and Majewski, Maciej and Husic, Brooke E. and Patel, Ankit and Fabritiis, Gianni De and Noé, Frank and Clementi, Cecilia (2023) Navigating protein landscapes with a machine-learned transferable coarse-grained model. Preprint . (Unpublished)

Arts, Marloes and Garcia Sattorras, Victor and Huang, Chin-Wei and Zuegner, Daniel and Federici, Marco and Clementi, Cecilia and Noé, Frank and Pinsler, Robert and van den Berg, Rianne (2023) Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. JCTC - Journal of Chemical Theory and Computation, 19 . pp. 6151-6159.

Majewski, Maciej and Pérez, Adrià and Thölke, Philipp and Doerr, Stefan and Charron, Nicholas E. and Giorgino, Toni and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank and De Fabritiis, Gianni (2023) Machine Learning Coarse-Grained Potentials of Protein Thermodynamics. Nature Communications, 14 .

Dyhr, Michael C. A. and Sadeghi, Mohsen and Moynova, Ralista and Knappe, Carolin and Burcu Kepsutlu, Çakmak and Werner, Stephan and Schneider, Gerd and McNally, James and Noé, Frank and Ewers, Helge (2023) 3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 120 (24).

Krämer, Andreas and Durumeric, Alexander E.P. and Charron, Nicholas E. and Chen, Yaoyi and Clementi, Cecilia and Noé, Frank (2023) Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The Journal of Physical Chemistry, 14 . pp. 3970-3979.

Durumeric, Alexander E.P. and Charron, Nicholas E. and Templeton, Clark and Musil, Félix and Bonneau, Klara and Pasos-Trejo, Aldo S. and Chen, Yaoyi and Kelkar, Atharva and Noé, Frank and Clementi, Cecilia (2023) Machine learned coarse-grained protein force-fields: Are we there yet? Current Opinion in Structural Biology, 79 .

Köhler, Jonas and Chen, Yaoyi and Krämer, Andreas and Clementi, Cecilia and Noé, Frank (2023) Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. J. Chem. Theory Comput., 19 (3). pp. 942-952.

Yang, Wangfei and Templeton, Clark and Rosenberger, David and Bittracher, Andreas and Nüske, Feliks and Noé, Frank and Clementi, Cecilia (2023) Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics. ACS Cent. Sci., 9 (2). pp. 186-196.

2022

Mardt, Andreas and Hempel, Tim and Clementi, Cecilia and Noé, Frank (2022) Deep learning to decompose macromolecules into independent Markovian domains. nature communications, 13 .

Musil, Félix and Zaporozhets, Iryna and Noé, Frank and Clementi, Cecilia and Kapil, Venkat (2022) Quantum dynamics using path integral coarse-graining. The Journal of Chemical Physics, 157 (18).

Dibak, Manuel and Klein, Leon and Krämer, Andreas and Noé, Frank (2022) Temperature steerable flows and Boltzmann generators. Physical Review Research, 4 (4).

2021

Kostré, Margarita and Schütte, Christof and Noé, Frank and del Razo, Mauricio J. (2021) Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs. Sociaty for Industrial and Applied Mathematics, 19 (4).

Sadeghi, Mohsen and Noé, Frank (2021) Thermodynamics and kinetics of aggregation of flexible peripheral membrane proteins. The Journal of Physical Chemistry Letters, 12 (43). pp. 10497-10504.

del Razo, Mauricio J. and Dibak, Manuel and Schütte, Christof and Noé, Frank (2021) Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics. The Journal of Chemical Physics, 155 (12).

Sadeghi, Mohsen and Noé, Frank (2021) Hydrodynamic coupling for particle-based solvent-free membrane models. The Journal of Chemical Physics, 155 (11).

Hempel, Tim and Elez, Katarina and Krüger, Nadine and Raich, Lluís and Shrimp, Jonathan H. and Danov, Olga and Jonigk, Danny and Braun, Arnim and Shen, Min and Hall, Matthew D. and Pöhlmann, Stefan and Hoffmann, Markus and Noé, Frank (2021) Synergistic inhibition of SARS-CoV-2 cell entry by otamixaban and covalent protease inhibitors: pre-clinical assessment of pharmacological and molecular properties. Chemical Science, 12 (38). pp. 12600-12609.

Chen, Yaoyi and Krämer, Andreas and Charron, Nicholas E. and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank (2021) Machine learning implicit solvation for molecular dynamics. The Journal of Chemical Physics, 155 (084101). pp. 1-15.

Klus, Stefan and Gelß, Patrick and Nüske, Feliks and Noé, Frank (2021) Symmetric and antisymmetric kernels for machine learning problems in quantum physics and chemistry. Machine Learning: Science and Technologie, 2 . pp. 1-23.

Azouz, Nurit P. and Klingler, Andrea M. and Callahan, Victoria and Akhrymuk, Ivan V. and Elez, Katarina and Raich, Lluís and Henry, Brandon M. and Benoit, Justin L. and Benoit, Stefanie W. and Noé, Frank and Kehn-Hall, Kylene and Rothenberg, Marc E. (2021) Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2. Pathogens and Immunity, 6 (1). pp. 55-74.

2020

Husic, Brooke E. and Charron, Nicholas E. and Lemm, Dominik and Wang, Jiang and Pérez, Adrià and Majewski, Maciej and Krämer, Andreas and Chen, Yaoyi and Olsson, Simon and de Fabritiis, Gianni and Noé, Frank and Clementi, Cecilia (2020) Coarse graining molecular dynamics with graph neural networks. J. Chem. Phys., 153 (194101). pp. 1-17.

Sadeghi, Mohsen and Noé, Frank (2020) Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models. Nature Communications, 11 (2951).

Noé, Frank (2020) Machine Learning for Molecular Dynamics on Long Timescales. Machine Learning Meets Quantum Physics . pp. 331-372.

Noé, Frank and Tkatchenko, Alexandre and Müller, Klaus-Robert and Clementi, Cecilia (2020) Machine Learning for Molecular Simulation. Annual Review of Physical Chemistry, 71 . pp. 361-390.

2019

Klus, Stefan and Husic, Brooke E. and Mollenhauer, Mattes and Noé, Frank (2019) Kernel methods for detecting coherent structures in dynamical data. Chaos, 29 (12).

Dibak, Manuel and Fröhner, Christoph and Noé, Frank and Höfling, Felix (2019) Diffusion-influenced reaction rates in the presence of pair interactions. The Journal of Chemical Physics, 151 (16).

Wu, Ho and Noé, Frank (2019) Variational approach for learning Markov processes from time series data. Journal of Nonlinear Science, 30 . pp. 23-66. ISSN 1432-1467 (online)

Kappler, Julian and Noé, Frank and Netz, Roland R. (2019) Cyclization and Relaxation Dynamics of Finite-Length Collapsed Self-Avoiding Polymers. Physical Review Letters, 122 .

0001

Galama, Maaike M. and Wu, Hao and Krämer, Andreas and Sadeghi, Mohsen and Noé, Frank (0001) Stochastic Approximation to MBAR and TRAM: Batchwise Free Energy Estimation. Journal of Chemical Theory and Computation (JCTC), 19 (3). pp. 758-766.