Related references
Note: Only part of the references are listed.Markov State Models Provide Insights into Dynamic Modulation of Protein Function
Diwakar Shukla et al.
ACCOUNTS OF CHEMICAL RESEARCH (2015)
Markov state models of biomolecular conformational dynamics
John D. Chodera et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2014)
Statistical Model Selection for Markov Models of Biomolecular Dynamics
Robert T. McGibbon et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Transition Paths of Met-Enkephalin from Markov State Modeling of a Molecular Dynamics Trajectory
Rahul Banerjee et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution
Benjamin Trendelkamp-Schroer et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Identification of slow molecular order parameters for Markov model construction
Guillermo Perez-Hernandez et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
Christian R. Schwantes et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
EMMA: A Software Package for Markov Model Building and Analysis
Martin Senne et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Simple few-state models reveal hidden complexity in protein folding
Kyle A. Beauchamp et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
IMPROVED INVERSE SCALING AND SQUARING ALGORITHMS FOR THE MATRIX LOGARITHM
Awad H. Al-Mohy et al.
SIAM JOURNAL ON SCIENTIFIC COMPUTING (2012)
Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz et al.
JOURNAL OF CHEMICAL PHYSICS (2011)
MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
Kyle A. Beauchamp et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein
Menahem Pirchi et al.
NATURE COMMUNICATIONS (2011)
Embeddable Markov Matrices
E. B. Davies
ELECTRONIC JOURNAL OF PROBABILITY (2010)
ON THE APPROXIMATION QUALITY OF MARKOV STATE MODELS
Marco Sarich et al.
MULTISCALE MODELING & SIMULATION (2010)
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw et al.
SCIENCE (2010)
DATA-BASED INFERENCE OF GENERATORS FOR MARKOV JUMP PROCESSES USING CONVEX OPTIMIZATION
Daan Crommelin et al.
MULTISCALE MODELING & SIMULATION (2009)
Using generalized ensemble simulations and Markov state models to identify conformational states
Gregory R. Bowman et al.
METHODS (2009)
Transition networks for modeling the kinetics of conformational change in macromolecules
Frank Noe et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)
An experimental survey of the transition between two-state and downhill protein folding scenarios
Feng Liu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Counting labeled transitions in continuous-time Markov models of evolution
Vladimir N. Minin et al.
JOURNAL OF MATHEMATICAL BIOLOGY (2008)
Generator estimation of Markov jump processes
P. Metzner et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2007)
Fitting timeseries by continuous-time Markov chains: A quadratic programming approach
D. T. Crommelin et al.
JOURNAL OF COMPUTATIONAL PHYSICS (2006)
Statistical inference for discretely observed Markov jump processes
M Bladt et al.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY (2005)
Describing protein folding kinetics by molecular dynamics simulations. 1. Theory
WC Swope et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
Evidence for sequential barriers and obligatory intermediates in apparent two-state protein folding
IE Sánchez et al.
JOURNAL OF MOLECULAR BIOLOGY (2003)
An expectation maximization algorithm for training hidden substitution models
I Holmes et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Finding generators for Markov chains via empirical transition matrices, with applications to credit ratings
RB Israel et al.
MATHEMATICAL FINANCE (2001)
Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains
P Deuflhard et al.
LINEAR ALGEBRA AND ITS APPLICATIONS (2000)