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Many state of the art methods for the thermodynamic and kinetic characterization of large and complex biomolecular systems by simulation rely on ensemble approaches, where data from large numbers of relatively short trajectories are integrated.
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Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory
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Meshless Methods in Conformation Dynamics
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Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States
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Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics
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Probability Distributions of Molecular Observables Computed from Markov Models
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Coarse Master Equations for Peptide Folding Dynamics
N.V. Buchete and G. Hummer · 2008
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Progress and Challenges in the Automated Construction of Markov State Models for Full Protein Systems
G. R. Bowman, K. A. Beauchamp, G. Boxer, and V. S. Pande · 2009
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Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations
F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and T.R. Weikl · 2009
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Statistical Error Estimation and Grid-free Hierarchical Refinement in Conformation Dynamics
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A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator
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Rapid equilibrium sampling initiated from nonequilibrium data
X. Huang, G. R. Bowman, S. Bacallado, and V. S. Pande · 2009
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Using generalized ensemble simulations and Markov state models to identify conformational states
G. R Bowman, X. Huang, and V. S. Pande · 2009
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ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
M. J. Harvey, G. Giupponi, and G. De Fabritiis · 2009
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Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9
V. A. Voelz, G. R. Bowman, K. Beauchamp, and V. S. Pande · 2010
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On the Approximation Quality of Markov State Models
M. Sarich, F. Noé, and C. Schütte · 2010
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Atomic-Level Characterization of the Structural Dynamics of Proteins
D.E. Shaw, P. Maragakis, K. Lindorff-Larsen, S. Piana, R.O. Dror, M.P. Eastwood, J.A. Bank, J.M. Jumper, J.K. Salmon, Y. Shan, and W. Wriggers · 2010
A Variational Approach to Modeling Slow Processes in Stochastic Dynamical Systems
F. Noé and F. Nüske · 2013
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Projected and Hidden Markov Models for Calculating Kinetics and Metastable States of Complex Molecules
F. Noé, H. Wu, J.-H. Prinz, and N. Plattner · 2013
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An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation
G. R. Bowman, V. S. Pande, and F. Noé, editors · 2014
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Variational Approach to Molecular Kinetics
F. Nüske, B. G. Keller, G. Pérez-Hernández, A. S. J. S. Mey, and F. Noé · 2014
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Fast Recovery of Free Energy Landscapes via Diffusion-Map-directed Molecular Dynamics
J. Preto and C. Clementi · 2014
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On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations
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Improved side-chain torsion potentials for the Amber ff99SB protein force field
K. Lindorff-Larsen, S. Piana, K. Palmo, P. Maragakis, J. L. Klepeis, R. O. Dror, and D. E. Shaw · 2010
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Markov Models of Molecular Kinetics: Generation and Validation
J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J. D. Chodera, C. Schütte, and F. Noé · 2011
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Simulating the T-Jump-Triggered Unfolding Dynamics of trpzip2 Peptide and Its Time-Resolved IR and Two-Dimensional IR Signals Using the Markov State Model Approach
W. Zhuang, R. Z. Cui, D.-A. Silva, and X. Huang · 2011
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How Fast-Folding Proteins Fold
K. Lindorff-Larsen, S. Piana, R. O. Dror, and D. E. Shaw · 2011
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Estimating the Eigenvalue Error of Markov State Models
N. Djurdjevac, M. Sarich, and C. Schütte · 2012
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Advanced Estimation Methods for Markov Models of Dynamical Systems
J.-H. Prinz · 2012
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S. Doerr and G. De Fabritiis · 2014
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Projected Metastable Markov Processes and their Estimation with Observable Operator Models
H. Wu, J.-H. Prinz, and F. Noé · 2015
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Estimation and Uncertainty of Reversible Markov Models
B. Trendelkamp-Schroer, H. Wu, F. Paul, and F. Noé · 2015
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Statistical inefficiency of Markov model count matrices
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PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
M. K. Scherer, B. Trendelkamp-Schroer, F. Paul, G. Pérez-Hernández, M. Hoffmann, N. Plattner, C. Wehmeyer, J.-H. Prinz, and F. Noé · 2015
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Dynamic properties of force fields
F. Vitalini, A. S. J. S. Mey, F. Noé, and B. G. Keller · 2015
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Spectral Learning of Dynamic Systems from Nonequilibrium Data
H. Wu and F. Noé · 2016
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HTMD: High-Throughput Molecular Dynamics for Molecular Discovery
S. Doerr, M. J. Harvey, F. Noé, and G. De Fabritiis · 2016
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