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Frank Noé - Publications

Affiliations: 
Department of Mathematics and Computer Science Freie Universität Berlin, Berlin, Germany 
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Year Citation  Score
2023 Majewski M, Pérez A, Thölke P, Doerr S, Charron NE, Giorgino T, Husic BE, Clementi C, Noé F, De Fabritiis G. Machine learning coarse-grained potentials of protein thermodynamics. Nature Communications. 14: 5739. PMID 37714883 DOI: 10.1038/s41467-023-41343-1  0.748
2023 Arts M, Garcia Satorras V, Huang CW, Zügner D, Federici M, Clementi C, Noé F, Pinsler R, van den Berg R. Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. Journal of Chemical Theory and Computation. 19: 6151-6159. PMID 37688551 DOI: 10.1021/acs.jctc.3c00702  0.303
2023 Hermann J, Spencer J, Choo K, Mezzacapo A, Foulkes WMC, Pfau D, Carleo G, Noé F. Ab initio quantum chemistry with neural-network wavefunctions. Nature Reviews. Chemistry. PMID 37558761 DOI: 10.1038/s41570-023-00516-8  0.682
2022 Mardt A, Hempel T, Clementi C, Noé F. Deep learning to decompose macromolecules into independent Markovian domains. Nature Communications. 13: 7101. PMID 36402768 DOI: 10.1038/s41467-022-34603-z  0.316
2022 Hempel T, Olsson S, Noé F. Markov field models: Scaling molecular kinetics approaches to large molecular machines. Current Opinion in Structural Biology. 77: 102458. PMID 36162297 DOI: 10.1016/j.sbi.2022.102458  0.336
2021 Mardt A, Noé F. Progress in deep Markov state modeling: Coarse graining and experimental data restraints. The Journal of Chemical Physics. 155: 214106. PMID 34879670 DOI: 10.1063/5.0064668  0.343
2021 Del Razo MJ, Dibak M, Schütte C, Noé F. Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics. The Journal of Chemical Physics. 155: 124109. PMID 34598578 DOI: 10.1063/5.0060314  0.351
2021 Chen Y, Krämer A, Charron NE, Husic BE, Clementi C, Noé F. Machine learning implicit solvation for molecular dynamics. The Journal of Chemical Physics. 155: 084101. PMID 34470360 DOI: 10.1063/5.0059915  0.746
2021 Hempel T, Del Razo MJ, Lee CT, Taylor BC, Amaro RE, Noé F. Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34321356 DOI: 10.1073/pnas.2105230118  0.32
2021 Glielmo A, Husic BE, Rodriguez A, Clementi C, Noé F, Laio A. Unsupervised Learning Methods for Molecular Simulation Data. Chemical Reviews. PMID 33945269 DOI: 10.1021/acs.chemrev.0c01195  0.731
2021 Wang J, Charron N, Husic B, Olsson S, Noé F, Clementi C. Multi-body effects in a coarse-grained protein force field. The Journal of Chemical Physics. 154: 164113. PMID 33940848 DOI: 10.1063/5.0041022  0.716
2021 Suárez E, Wiewiora RP, Wehmeyer C, Noé F, Chodera JD, Zuckerman DM. What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models. Journal of Chemical Theory and Computation. PMID 33904312 DOI: 10.1021/acs.jctc.0c01154  0.308
2020 Husic BE, Charron NE, Lemm D, Wang J, Pérez A, Majewski M, Krämer A, Chen Y, Olsson S, de Fabritiis G, Noé F, Clementi C. Coarse graining molecular dynamics with graph neural networks. The Journal of Chemical Physics. 153: 194101. PMID 33218238 DOI: 10.1063/5.0026133  0.718
2020 Hermann J, Schätzle Z, Noé F. Deep-neural-network solution of the electronic Schrödinger equation. Nature Chemistry. 12: 891-897. PMID 32968231 DOI: 10.1038/s41557-020-0544-y  0.673
2020 Sadeghi M, Noé F. Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models. Nature Communications. 11: 2951. PMID 32528158 DOI: 10.1038/S41467-020-16424-0  0.403
2020 Hempel T, Plattner N, Noé F. Coupling of conformational switches in calcium sensor unraveled with local Markov models and transfer entropy. Journal of Chemical Theory and Computation. PMID 32196329 DOI: 10.1021/Acs.Jctc.0C00043  0.323
2020 Noé F, Tkatchenko A, Müller KR, Clementi C. Machine Learning for Molecular Simulation. Annual Review of Physical Chemistry. PMID 32092281 DOI: 10.1146/Annurev-Physchem-042018-052331  0.61
2020 Wang J, Chmiela S, Müller K, Noé F, Clementi C. Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach The Journal of Chemical Physics. 152: 194106. DOI: 10.1063/5.0007276  0.338
2020 Le T, Winter R, Noe F, Clevert D. Neuraldecipher – reverse-engineering extended-connectivity fingerprints (ECFPs) to their molecular structures Chemical Science. DOI: 10.1039/D0Sc03115A  0.35
2019 Klus S, Husic BE, Mollenhauer M, Noé F. Kernel methods for detecting coherent structures in dynamical data. Chaos (Woodbury, N.Y.). 29: 123112. PMID 31893642 DOI: 10.1063/1.5100267  0.748
2019 Noé F, De Fabritiis G, Clementi C. Machine learning for protein folding and dynamics. Current Opinion in Structural Biology. 60: 77-84. PMID 31881449 DOI: 10.1016/J.Sbi.2019.12.005  0.379
2019 Winter R, Montanari F, Steffen A, Briem H, Noé F, Clevert DA. Efficient multi-objective molecular optimization in a continuous latent space. Chemical Science. 10: 8016-8024. PMID 31853357 DOI: 10.1039/C9Sc01928F  0.315
2019 Noé F, Rosta E. Markov Models of Molecular Kinetics. The Journal of Chemical Physics. 151: 190401. PMID 31757166 DOI: 10.1063/1.5134029  0.368
2019 Dibak M, Fröhner C, Noé F, Höfling F. Diffusion-influenced reaction rates in the presence of pair interactions. The Journal of Chemical Physics. 151: 164105. PMID 31675872 DOI: 10.1063/1.5124728  0.344
2019 Noel JK, Noé F, Daumke O, Mikhailov AS. Polymer-like Model to Study the Dynamics of Dynamin Filaments on Deformable Membrane Tubes. Biophysical Journal. PMID 31672269 DOI: 10.1016/J.Bpj.2019.09.042  0.327
2019 Zhang J, Yang YI, Noé F. Targeted Adversarial Learning Optimized Sampling. The Journal of Physical Chemistry Letters. PMID 31522495 DOI: 10.1021/Acs.Jpclett.9B02173  0.384
2019 Noé F, Olsson S, Köhler J, Wu H. Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning. Science (New York, N.Y.). 365. PMID 31488660 DOI: 10.1126/Science.Aaw1147  0.39
2019 Olsson S, Noé F. Dynamic graphical models of molecular kinetics. Proceedings of the National Academy of Sciences of the United States of America. PMID 31285323 DOI: 10.1073/Pnas.1901692116  0.431
2019 Wang J, Olsson S, Wehmeyer C, Pérez A, Charron NE, de Fabritiis G, Noé F, Clementi C. Machine Learning of Coarse-Grained Molecular Dynamics Force Fields. Acs Central Science. 5: 755-767. PMID 31139712 DOI: 10.1021/Acscentsci.8B00913  0.4
2019 Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott T, Baker BM. Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility. Frontiers in Immunology. 10: 966. PMID 31130956 DOI: 10.3389/Fimmu.2019.00966  0.308
2019 Scherer MK, Husic BE, Hoffmann M, Paul F, Wu H, Noé F. Variational selection of features for molecular kinetics. The Journal of Chemical Physics. 150: 194108. PMID 31117766 DOI: 10.1063/1.5083040  0.759
2019 Paul F, Wu H, Vossel M, de Groot BL, Noé F. Identification of kinetic order parameters for non-equilibrium dynamics. The Journal of Chemical Physics. 150: 164120. PMID 31042914 DOI: 10.1063/1.5083627  0.444
2019 Pinamonti G, Paul F, Noé F, Rodriguez A, Bussi G. The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. The Journal of Chemical Physics. 150: 154123. PMID 31005065 DOI: 10.1063/1.5083227  0.389
2019 Winter R, Montanari F, Noé F, Clevert DA. Learning continuous and data-driven molecular descriptors by translating equivalent chemical representations. Chemical Science. 10: 1692-1701. PMID 30842833 DOI: 10.1039/C8Sc04175J  0.345
2019 Kappler J, Noé F, Netz RR. Cyclization and Relaxation Dynamics of Finite-Length Collapsed Self-Avoiding Polymers. Physical Review Letters. 122: 067801. PMID 30822085 DOI: 10.1103/Physrevlett.122.067801  0.311
2019 Hoffmann M, Fröhner C, Noé F. ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. Plos Computational Biology. 15: e1006830. PMID 30818351 DOI: 10.1371/Journal.Pcbi.1006830  0.406
2019 Hoffmann M, Fröhner C, Noé F. Reactive SINDy: Discovering governing reactions from concentration data. The Journal of Chemical Physics. 150: 025101. PMID 30646700 DOI: 10.1063/1.5066099  0.309
2019 Husic BE, Noé F. Deflation reveals dynamical structure in nondominant reaction coordinates The Journal of Chemical Physics. 151: 054103. DOI: 10.1063/1.5099194  0.766
2019 Noé F. Machine Learning Methods to Push All-Atom MD Beyond the Seconds Timescale and Simulate Protein-Protein Association and Dissociation Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.1795  0.343
2019 Wu H, Noé F. Variational Approach for Learning Markov Processes from Time Series Data Journal of Nonlinear Science. 30: 23-66. DOI: 10.1007/S00332-019-09567-Y  0.391
2018 Schulz R, von Hansen Y, Daldrop JO, Kappler J, Noé F, Netz RR. Collective hydrogen-bond rearrangement dynamics in liquid water. The Journal of Chemical Physics. 149: 244504. PMID 30599706 DOI: 10.1063/1.5054267  0.304
2018 Swenson D, Prinz JH, Noé F, Chodera JD, Bolhuis PG. OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemes. Journal of Chemical Theory and Computation. PMID 30359525 DOI: 10.1021/Acs.Jctc.8B00627  0.315
2018 Swenson D, Prinz JH, Noé F, Chodera JD, Bolhuis PG. OpenPathSampling: A Python framework for path sampling simulations. I. Basics. Journal of Chemical Theory and Computation. PMID 30336030 DOI: 10.1021/Acs.Jctc.8B00626  0.365
2018 Fröhner C, Noé F. Reversible Interacting-Particle Reaction Dynamics. The Journal of Physical Chemistry. B. PMID 30125111 DOI: 10.1021/Acs.Jpcb.8B06981  0.38
2018 Qureshi BM, Behrmann E, Schöneberg J, Loerke J, Bürger J, Mielke T, Giesebrecht J, Noé F, Lamb TD, Hofmann KP, Spahn CMT, Heck M. It takes two transducins to activate the cGMP-phosphodiesterase 6 in retinal rods. Open Biology. 8. PMID 30068566 DOI: 10.1098/Rsob.180075  0.72
2018 Del Razo MJ, Qian H, Noé F. Grand canonical diffusion-influenced reactions: A stochastic theory with applications to multiscale reaction-diffusion simulations. The Journal of Chemical Physics. 149: 044102. PMID 30068197 DOI: 10.1063/1.5037060  0.37
2018 Wehmeyer C, Noé F. Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics. The Journal of Chemical Physics. 148: 241703. PMID 29960344 DOI: 10.1063/1.5011399  0.35
2018 Dibak M, Del Razo MJ, De Sancho D, Schütte C, Noé F. MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. The Journal of Chemical Physics. 148: 214107. PMID 29884049 DOI: 10.1063/1.5020294  0.448
2018 Litzinger F, Boninsegna L, Wu H, Nüske F, Patel R, Baraniuk R, Noé F, Clementi C. Rapid calculation of molecular kinetics using compressed sensing. Journal of Chemical Theory and Computation. PMID 29660273 DOI: 10.1021/Acs.Jctc.8B00089  0.393
2018 Paul F, Wehmeyer C, Abualrous ET, Wu H, Crabtree MD, Schöneberg J, Clarke J, Freund C, Weikl TR, Noé F. Author Correction: Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nature Communications. 9: 1073. PMID 29523780 DOI: 10.1038/S41467-018-03452-0  0.704
2018 Paul F, Noé F, Weikl TR. Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations. The Journal of Physical Chemistry. B. PMID 29522679 DOI: 10.1021/Acs.Jpcb.7B12146  0.326
2018 Sadeghi M, Weikl TR, Noé F. Particle-based membrane model for mesoscopic simulation of cellular dynamics. The Journal of Chemical Physics. 148: 044901. PMID 29390800 DOI: 10.1063/1.5009107  0.39
2018 Gerber S, Olsson S, Noé F, Horenko I. A scalable approach to the computation of invariant measures for high-dimensional Markovian systems. Scientific Reports. 8: 1796. PMID 29379123 DOI: 10.1038/S41598-018-19863-4  0.362
2018 Mardt A, Pasquali L, Wu H, Noé F. VAMPnets for deep learning of molecular kinetics. Nature Communications. 9: 5. PMID 29295994 DOI: 10.1038/S41467-017-02388-1  0.466
2018 Koltai P, Wu H, Noé F, Schütte C. Optimal Data-Driven Estimation of Generalized Markov State Models for Non-Equilibrium Dynamics Computation. 6: 22. DOI: 10.3390/Computation6010022  0.42
2018 Klus S, Nüske F, Koltai P, Wu H, Kevrekidis I, Schütte C, Noé F. Data-Driven Model Reduction and Transfer Operator Approximation Journal of Nonlinear Science. 28: 985-1010. DOI: 10.1007/S00332-017-9437-7  0.356
2017 Sbailò L, Noé F. An efficient multi-scale Green's function reaction dynamics scheme. The Journal of Chemical Physics. 147: 184106. PMID 29141429 DOI: 10.1063/1.5010190  0.394
2017 Paul F, Wehmeyer C, Abualrous ET, Wu H, Crabtree MD, Schöneberg J, Clarke J, Freund C, Weikl TR, Noé F. Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nature Communications. 8: 1095. PMID 29062047 DOI: 10.1038/S41467-017-01163-6  0.754
2017 Plattner N, Doerr S, De Fabritiis G, Noé F. Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nature Chemistry. 9: 1005-1011. PMID 28937668 DOI: 10.1038/Nchem.2785  0.448
2017 Olsson S, Wu H, Paul F, Clementi C, Noé F. Combining experimental and simulation data of molecular processes via augmented Markov models. Proceedings of the National Academy of Sciences of the United States of America. PMID 28716931 DOI: 10.1073/Pnas.1704803114  0.423
2017 Schöneberg J, Lehmann M, Ullrich A, Posor Y, Lo WT, Lichtner G, Schmoranzer J, Haucke V, Noé F. Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nature Communications. 8: 15873. PMID 28627515 DOI: 10.1038/Ncomms15873  0.708
2017 Abramyan AM, Stolzenberg S, Li Z, Loland CJ, Noé F, Shi L. The isomeric preference of an atypical dopamine transporter inhibitor contributes to its selection of the transporter conformation. Acs Chemical Neuroscience. PMID 28441487 DOI: 10.1021/Acschemneuro.7B00094  0.335
2017 Wu H, Nüske F, Paul F, Klus S, Koltai P, Noé F. Variational Koopman models: Slow collective variables and molecular kinetics from short off-equilibrium simulations. The Journal of Chemical Physics. 146: 154104. PMID 28433026 DOI: 10.1063/1.4979344  0.449
2017 Noé F, Clementi C. Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods. Current Opinion in Structural Biology. 43: 141-147. PMID 28327454 DOI: 10.1016/J.Sbi.2017.02.006  0.391
2017 Nüske F, Wu H, Prinz J, Wehmeyer C, Clementi C, Noé F. Markov state models from short non-equilibrium simulations—Analysis and correction of estimation bias The Journal of Chemical Physics. 146: 094104. DOI: 10.1063/1.4976518  0.394
2016 Pinamonti G, Zhao J, Condon DE, Paul F, Noé F, Turner DH, Bussi G. Predicting the kinetics of RNA oligonucleotides using Markov state models. Journal of Chemical Theory and Computation. PMID 28001394 DOI: 10.1021/Acs.Jctc.6B00982  0.403
2016 Olsson S, Noé F. Mechanistic models of chemical exchange induced relaxation in protein NMR. Journal of the American Chemical Society. PMID 27958728 DOI: 10.1021/Jacs.6B09460  0.433
2016 Wieczorek M, Sticht J, Stolzenberg S, Günther S, Wehmeyer C, El Habre Z, Álvaro-Benito M, Noé F, Freund C. MHC class II complexes sample intermediate states along the peptide exchange pathway. Nature Communications. 7: 13224. PMID 27827392 DOI: 10.1038/Ncomms13224  0.329
2016 Pérez-Hérnandez G, Noé F. Hierarchical time-lagged independent component analysis: computing slow modes and reaction coordinates for large molecular systems. Journal of Chemical Theory and Computation. PMID 27792332 DOI: 10.1021/Acs.Jctc.6B00738  0.39
2016 Noé F, Banisch R, Clementi C. Commute maps: separating slowly-mixing molecular configurations for kinetic modeling. Journal of Chemical Theory and Computation. PMID 27696838 DOI: 10.1021/Acs.Jctc.6B00762  0.408
2016 Wu H, Paul F, Wehmeyer C, Noé F. Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences of the United States of America. PMID 27226302 DOI: 10.1073/Pnas.1525092113  0.445
2016 Vitalini F, Noé F, Keller BG. Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data in Brief. 7: 582-90. PMID 27054161 DOI: 10.1016/J.Dib.2016.02.086  0.359
2016 Doerr S, Harvey MJ, Noé F, De Fabritiis G. HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. Journal of Chemical Theory and Computation. 12: 1845-52. PMID 26949976 DOI: 10.1021/Acs.Jctc.6B00049  0.445
2016 Nüske F, Schneider R, Vitalini F, Noé F. Variational tensor approach for approximating the rare-event kinetics of macromolecular systems. The Journal of Chemical Physics. 144: 054105. PMID 26851906 DOI: 10.1063/1.4940774  0.357
2016 Trendelkamp-Schroer B, Noé F. Efficient estimation of rare-event kinetics Physical Review X. 6: 11009. DOI: 10.1103/Physrevx.6.011009  0.332
2015 Boninsegna L, Gobbo G, Noé F, Clementi C. Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps. Journal of Chemical Theory and Computation. 11: 5947-60. PMID 26580713 DOI: 10.1021/Acs.Jctc.5B00749  0.369
2015 Vitalini F, Noé F, Keller BG. A Basis Set for Peptides for the Variational Approach to Conformational Kinetics. Journal of Chemical Theory and Computation. 11: 3992-4004. PMID 26575895 DOI: 10.1021/Acs.Jctc.5B00498  0.362
2015 Scherer MK, Trendelkamp-Schroer B, Paul F, Pérez-Hernández G, Hoffmann M, Plattner N, Wehmeyer C, Prinz JH, Noé F. PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. Journal of Chemical Theory and Computation. 11: 5525-42. PMID 26574340 DOI: 10.1021/Acs.Jctc.5B00743  0.426
2015 Noé F, Clementi C. Kinetic distance and kinetic maps from molecular dynamics simulation. Journal of Chemical Theory and Computation. 11: 5002-11. PMID 26574285 DOI: 10.1021/Acs.Jctc.5B00553  0.451
2015 Trendelkamp-Schroer B, Wu H, Paul F, Noé F. Estimation and uncertainty of reversible Markov models. The Journal of Chemical Physics. 143: 174101. PMID 26547152 DOI: 10.1063/1.4934536  0.36
2015 Wu H, Prinz JH, Noé F. Projected metastable Markov processes and their estimation with observable operator models. The Journal of Chemical Physics. 143: 144101. PMID 26472357 DOI: 10.1063/1.4932406  0.41
2015 Ullrich A, Böhme MA, Schöneberg J, Depner H, Sigrist SJ, Noé F. Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone. Plos Computational Biology. 11: e1004407. PMID 26367029 DOI: 10.1371/Journal.Pcbi.1004407  0.705
2015 Reubold TF, Faelber K, Plattner N, Posor Y, Ketel K, Curth U, Schlegel J, Anand R, Manstein DJ, Noé F, Haucke V, Daumke O, Eschenburg S. Crystal structure of the dynamin tetramer. Nature. 525: 404-8. PMID 26302298 DOI: 10.1038/Nature14880  0.358
2015 Schor M, Mey AS, Noé F, MacPhee CE. Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models. The Journal of Physical Chemistry Letters. 6: 1076-81. PMID 26262873 DOI: 10.1021/Acs.Jpclett.5B00330  0.342
2015 Plattner N, Noé F. Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nature Communications. 6: 7653. PMID 26134632 DOI: 10.1038/Ncomms8653  0.367
2015 Gunkel M, Schöneberg J, Alkhaldi W, Irsen S, Noé F, Kaupp UB, Al-Amoudi A. Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure (London, England : 1993). 23: 628-38. PMID 25728926 DOI: 10.1016/J.Str.2015.01.015  0.73
2015 Wu H, Noé F. Gaussian Markov transition models of molecular kinetics. The Journal of Chemical Physics. 142: 084104. PMID 25725709 DOI: 10.1063/1.4913214  0.401
2015 Vitalini F, Mey AS, Noé F, Keller BG. Dynamic properties of force fields. The Journal of Chemical Physics. 142: 084101. PMID 25725706 DOI: 10.1063/1.4909549  0.401
2015 Schöneberg J, Hofmann KP, Heck M, Noé F. Response to comment "Transient complexes between dark rhodopsin and transducin: circumstantial evidence or physiological necessity?" by D. Dell'Orco and K.-W. Koch. Biophysical Journal. 108: 778-9. PMID 25650945 DOI: 10.1016/J.Bpj.2014.12.030  0.717
2015 Biedermann J, Ullrich A, Schöneberg J, Noé F. ReaDDyMM: Fast interacting particle reaction-diffusion simulations using graphical processing units. Biophysical Journal. 108: 457-61. PMID 25650912 DOI: 10.1016/J.Bpj.2014.12.025  0.744
2015 Noé F. Beating the millisecond barrier in molecular dynamics simulations. Biophysical Journal. 108: 228-9. PMID 25606670 DOI: 10.1016/J.Bpj.2014.11.3477  0.385
2015 Qureshi BM, Behrmann E, Schöneberg J, Loerke J, Bürger J, Mielke T, Giesebrecht J, Noé F, Hofmann KP, Spahn CMT, Heck M. Asymmetric properties of rod cGMP Phosphodiesterase 6 (PDE6): structural and functional analysis Bmc Pharmacology and Toxicology. 16. DOI: 10.1186/2050-6511-16-S1-A76  0.716
2014 Nüske F, Keller BG, Pérez-Hernández G, Mey AS, Noé F. Variational Approach to Molecular Kinetics. Journal of Chemical Theory and Computation. 10: 1739-52. PMID 26580382 DOI: 10.1021/Ct4009156  0.386
2014 Schöneberg J, Ullrich A, Noé F. Simulation tools for particle-based reaction-diffusion dynamics in continuous space. Bmc Biophysics. 7: 11. PMID 25737778 DOI: 10.1186/S13628-014-0011-5  0.735
2014 Wu H, Mey AS, Rosta E, Noé F. Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. The Journal of Chemical Physics. 141: 214106. PMID 25481128 DOI: 10.1063/1.4902240  0.352
2014 Prinz JH, Chodera JD, Noé F. Spectral Rate Theory for Two-State Kinetics. Physical Review. X. 4. PMID 25356374 DOI: 10.1103/Physrevx.4.011020  0.362
2014 Schöneberg J, Heck M, Hofmann KP, Noé F. Explicit spatiotemporal simulation of receptor-G protein coupling in rod cell disk membranes. Biophysical Journal. 107: 1042-53. PMID 25185540 DOI: 10.1016/J.Bpj.2014.05.050  0.712
2014 Chodera JD, Noé F. Markov state models of biomolecular conformational dynamics. Current Opinion in Structural Biology. 25: 135-44. PMID 24836551 DOI: 10.1016/J.Sbi.2014.04.002  0.468
2014 Bowman GR, Noé F. Software for building Markov state models. Advances in Experimental Medicine and Biology. 797: 139. PMID 24297281 DOI: 10.1007/978-94-007-7606-7_11  0.306
2014 Noé F, Prinz JH. Analysis of Markov models. Advances in Experimental Medicine and Biology. 797: 75-90. PMID 24297276 DOI: 10.1007/978-94-007-7606-7_6  0.371
2014 Prinz JH, Chodera JD, Noé F. Estimation and validation of Markov models. Advances in Experimental Medicine and Biology. 797: 45-60. PMID 24297274 DOI: 10.1007/978-94-007-7606-7_4  0.348
2014 Bowman GR, Pande VS, Noé F. Introduction and overview of this book Advances in Experimental Medicine and Biology. 797: 1-6. PMID 24297271 DOI: 10.1007/978-94-007-7606-7_1  0.425
2014 Wu H, Noé F. Optimal Estimation of Free Energies and Stationary Densities from Multiple Biased Simulations Multiscale Modeling & Simulation. 12: 25-54. DOI: 10.1137/120895883  0.374
2014 Mey AS, Wu H, Noé F. xTRAM: Estimating Equilibrium Expectations from Time-Correlated Simulation Data at Multiple Thermodynamic States Physical Review X. 4. DOI: 10.1103/Physrevx.4.041018  0.405
2013 Noé F, Wu H, Prinz JH, Plattner N. Projected and hidden Markov models for calculating kinetics and metastable states of complex molecules. The Journal of Chemical Physics. 139: 184114. PMID 24320261 DOI: 10.1063/1.4828816  0.451
2013 Yi Z, Lindner B, Prinz JH, Noé F, Smith JC. Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling. The Journal of Chemical Physics. 139: 175102. PMID 24206335 DOI: 10.1063/1.4824071  0.56
2013 Lindner B, Yi Z, Prinz JH, Smith JC, Noé F. Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models. The Journal of Chemical Physics. 139: 175101. PMID 24206334 DOI: 10.1063/1.4824070  0.528
2013 Schöneberg J, Noé F. ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments. Plos One. 8: e74261. PMID 24040218 DOI: 10.1371/Journal.Pone.0074261  0.76
2013 Pérez-Hernández G, Paul F, Giorgino T, De Fabritiis G, Noé F. Identification of slow molecular order parameters for Markov model construction. The Journal of Chemical Physics. 139: 015102. PMID 23822324 DOI: 10.1063/1.4811489  0.414
2013 Steger K, Bollmann S, Noé F, Doose S. Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale. Physical Chemistry Chemical Physics : Pccp. 15: 10435-45. PMID 23685745 DOI: 10.1039/C3Cp50644D  0.304
2013 Faelber K, Gao S, Held M, Posor Y, Haucke V, Noé F, Daumke O. Oligomerization of dynamin superfamily proteins in health and disease. Progress in Molecular Biology and Translational Science. 117: 411-43. PMID 23663977 DOI: 10.1016/B978-0-12-386931-9.00015-5  0.303
2013 Trendelkamp-Schroer B, Noé F. Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution. The Journal of Chemical Physics. 138: 164113. PMID 23635117 DOI: 10.1063/1.4801325  0.431
2013 Noé F, Nüske F. A variational approach to modeling slow processes in stochastic dynamical systems Multiscale Modeling & Simulation. 11: 635-655. DOI: 10.1137/110858616  0.407
2012 Senne M, Trendelkamp-Schroer B, Mey AS, Schütte C, Noé F. EMMA: A Software Package for Markov Model Building and Analysis. Journal of Chemical Theory and Computation. 8: 2223-38. PMID 26588955 DOI: 10.1021/Ct300274U  0.416
2012 Sadiq SK, Noé F, De Fabritiis G. Kinetic characterization of the critical step in HIV-1 protease maturation. Proceedings of the National Academy of Sciences of the United States of America. 109: 20449-54. PMID 23184967 DOI: 10.1073/Pnas.1210983109  0.314
2012 Faelber K, Held M, Gao S, Posor Y, Haucke V, Noé F, Daumke O. Structural insights into dynamin-mediated membrane fission. Structure (London, England : 1993). 20: 1621-8. PMID 23063009 DOI: 10.1016/J.Str.2012.08.028  0.327
2012 Held M, Imhof P, Keller BG, Noé F. Modulation of a ligand's energy landscape and kinetics by the chemical environment. The Journal of Physical Chemistry. B. 116: 13597-607. PMID 23025812 DOI: 10.1021/Jp3006684  0.395
2012 Held M, Noé F. Calculating kinetics and pathways of protein-ligand association. European Journal of Cell Biology. 91: 357-64. PMID 22018914 DOI: 10.1016/J.Ejcb.2011.08.004  0.342
2012 Keller BG, Prinz JH, Noé F. Markov models and dynamical fingerprints: Unraveling the complexity of molecular kinetics Chemical Physics. 396: 92-107. DOI: 10.1016/J.Chemphys.2011.08.021  0.44
2012 Peuker S, Held M, Cukkemane A, Noe F, Kaupp UB, Seifert R. Kinetics of Ligand Receptor Interaction Reveals the Mode of Binding in Cyclic Nucleotide-Activated Proteins Biophysical Journal. 102. DOI: 10.1016/J.Bpj.2011.11.2521  0.305
2011 Prinz JH, Keller B, Noé F. Probing molecular kinetics with Markov models: metastable states, transition pathways and spectroscopic observables. Physical Chemistry Chemical Physics : Pccp. 13: 16912-27. PMID 21858310 DOI: 10.1039/C1Cp21258C  0.443
2011 Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. The Journal of Chemical Physics. 134: 244108. PMID 21721613 DOI: 10.1063/1.3592153  0.626
2011 Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. The Journal of Chemical Physics. 134: 244107. PMID 21721612 DOI: 10.1063/1.3592152  0.57
2011 Schütte C, Noé F, Lu J, Sarich M, Vanden-Eijnden E. Markov state models based on milestoning. The Journal of Chemical Physics. 134: 204105. PMID 21639422 DOI: 10.1063/1.3590108  0.368
2011 Splettstoesser T, Holmes KC, Noé F, Smith JC. Structural modeling and molecular dynamics simulation of the actin filament. Proteins. 79: 2033-43. PMID 21557314 DOI: 10.1002/Prot.23017  0.515
2011 Prinz JH, Wu H, Sarich M, Keller B, Senne M, Held M, Chodera JD, Schütte C, Noé F. Markov models of molecular kinetics: generation and validation. The Journal of Chemical Physics. 134: 174105. PMID 21548671 DOI: 10.1063/1.3565032  0.447
2011 Wu H, Noé F. Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 83: 036705. PMID 21517623 DOI: 10.1103/Physreve.83.036705  0.343
2011 Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proceedings of the National Academy of Sciences of the United States of America. 108: 4822-7. PMID 21368203 DOI: 10.1073/Pnas.1004646108  0.553
2011 Held M, Metzner P, Prinz JH, Noé F. Mechanisms of protein-ligand association and its modulation by protein mutations. Biophysical Journal. 100: 701-10. PMID 21281585 DOI: 10.1016/J.Bpj.2010.12.3699  0.322
2011 Prinz JH, Held M, Smith JC, Noé F. Efficient computation, sensitivity, and error analysis of committor probabilities for complex dynamical processes Multiscale Modeling and Simulation. 9: 545-567. DOI: 10.1137/100789191  0.526
2010 Chodera JD, Noé F. Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution. The Journal of Chemical Physics. 133: 105102. PMID 20849191 DOI: 10.1063/1.3463406  0.405
2010 Bernhard S, Noé F. Optimal identification of semi-rigid domains in macromolecules from molecular dynamics simulation. Plos One. 5: e10491. PMID 20498702 DOI: 10.1371/Journal.Pone.0010491  0.41
2010 Wu H, Noé F. Probability Distance Based Compression of Hidden Markov Models Multiscale Modeling & Simulation. 8: 1838-1861. DOI: 10.1137/090774161  0.376
2010 Sarich M, Noé F, Schütte C. On The Approximation Quality Of Markov State Models Multiscale Modeling & Simulation. 8: 1154-1177. DOI: 10.1137/090764049  0.378
2010 Splettstoesser T, Holmes KC, Noé F, Smith JC. A Comparison of Actin Filament Models by Molecular Dynamics Simulation Biophysical Journal. 98: 154a. DOI: 10.1016/J.Bpj.2009.12.826  0.498
2009 Noé F, Schütte C, Vanden-Eijnden E, Reich L, Weikl TR. Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations Proceedings of the National Academy of Sciences of the United States of America. 106: 19011-19016. PMID 19887634 DOI: 10.1073/Pnas.0905466106  0.439
2009 Metzner P, Noé F, Schütte C. Estimating the sampling error: distribution of transition matrices and functions of transition matrices for given trajectory data. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 80: 021106. PMID 19792076 DOI: 10.1103/Physreve.80.021106  0.339
2009 Splettstoesser T, Noé F, Oda T, Smith JC. Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state. Proteins. 76: 353-64. PMID 19156817 DOI: 10.1002/Prot.22350  0.48
2008 Noé F, Daidone I, Smith JC, di Nola A, Amadei A. Solvent electrostriction-driven peptide folding revealed by quasi-Gaussian entropy theory and molecular dynamics simulation. The Journal of Physical Chemistry. B. 112: 11155-63. PMID 18698708 DOI: 10.1021/Jp801391T  0.504
2008 Noé F. Probability distributions of molecular observables computed from Markov models. The Journal of Chemical Physics. 128: 244103. PMID 18601313 DOI: 10.1063/1.2916718  0.397
2008 Noé F, Fischer S. Transition networks for modeling the kinetics of conformational change in macromolecules. Current Opinion in Structural Biology. 18: 154-62. PMID 18378442 DOI: 10.1016/J.Sbi.2008.01.008  0.375
2007 Horenko I, Hartmann C, Schütte C, Noe F. Data-based parameter estimation of generalized multidimensional Langevin processes. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 76: 016706. PMID 17677593 DOI: 10.1103/Physreve.76.016706  0.352
2007 Noé F, Horenko I, Schütte C, Smith JC. Hierarchical analysis of conformational dynamics in biomolecules: transition networks of metastable states. The Journal of Chemical Physics. 126: 155102. PMID 17461666 DOI: 10.1063/1.2714539  0.577
2006 Imhof P, Noé F, Fischer S, Smith JC. AM1/d Parameters for Magnesium in Metalloenzymes. Journal of Chemical Theory and Computation. 2: 1050-6. PMID 26633065 DOI: 10.1021/Ct600092C  0.446
2006 Noé F, Krachtus D, Smith JC, Fischer S. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. Journal of Chemical Theory and Computation. 2: 840-57. PMID 26626691 DOI: 10.1021/Ct050162R  0.48
2006 Noé F, Oswald M, Reinelt G, Fischer S, Smith JC. Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the AlphaL \leftrightharpoons Beta \leftrightharpoons AlphaR Transitions in Octaalanine Multiscale Modeling & Simulation. 5: 393-419. DOI: 10.1137/050641922  0.494
2005 Noé F, Ille F, Smith JC, Fischer S. Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21. Proteins. 59: 534-44. PMID 15778967 DOI: 10.1002/Prot.20422  0.511
2003 Noé F, Schwarzl SM, Fischer S, Smith JC. Computational tools for analysing structural changes in proteins in solution. Applied Bioinformatics. 2: S11-7. PMID 15130811  0.431
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