Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states.
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Summary
dTRAM provides maximum-likelihood estimates of stationary quantities (probabilities, free energies, expectation values) at any thermodynamic state and provides optimal estimates of Markov state models (MSMs) from the discretized state-space trajectories at all thermodynamic states.
- Type
- article
- Published
- 2014-11-11
- Cited by
- 81
- References
- 53
- Access
- Open access
- OpenAlex
- https://openalex.org/W2054177481
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:5656166
Keywords
Trajectory, Limit (mathematics), Discretization, Generalization, Markov chain
References
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- Optimized Monte Carlo data analysis.
- Exchange Monte Carlo Method and Application to Spin Glass Simulations
- Statistically optimal analysis of samples from multiple equilibrium states.
- Coarse master equations for peptide folding dynamics.
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- Replica-exchange molecular dynamics method for protein folding
- Adaptive single replica multiple state transition interface sampling.
Cited by
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- Microscopic Characterization of Membrane Transporter Function by in silico Modeling and Simulation
- Estimation and uncertainty of reversible Markov models.
- Efficient estimation of rare-event kinetics
- PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models.
- Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models
- Reversible Markov chain estimation using convex-concave programming
- Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation.
- Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue
- Enhancing pairwise state-transition weights: A new weighting scheme in simulated tempering that can minimize transition time between a pair of conformational states.
- Multiensemble Markov models of molecular thermodynamics and kinetics
- A Maximum-Caliber Approach to Predicting Perturbed Folding Kinetics Due to Mutations.
- A Stochastic Solution to the Unbinned WHAM Equations
- Elucidation of the conformational dynamics of multi-body systems by construction of Markov state models.
- QM/MM free energy simulations: recent progress and challenges
- The Dynamic Basis for Signal Propagation in Human Pin1-WW.
- Transition path theory analysis of c-Src kinase activation
- Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins
- First passage times and relaxation times of unfolded proteins and the funnel model of protein folding
- Methodological aspects of the calculation of the free energy profile of guanosine triphosphate hydrolysis by Ras-GAP protein complex
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