Markov state models based on milestoning

Cited by (227)

Items 201–227 of 227

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2. Equilibrium and Nonequilibrium Methods for Free-Energy Calculations With Molecular Dynamics
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3. Determination of Kinetics and Thermodynamics of Biomolecular Processes with Trajectory Fragments
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4. Mathematical Foundations of Accelerated Molecular Dynamics Methods
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5. Advanced estimation methods for Markov models of dynamical systems
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6. Molecular mechanism of the pH-dependent calcium affinity in langerin
   Jan-O. Joswig, J. Anders, Hengxi Zhang, C. Rademacher, B. Keller · 2020 · bioRxiv
7. Unbiased estimation of equilibrium, rates, and committors from Markov state model analysis
   John D. Russo, Jeremy Copperman, David Aristoff, Gideon Simpson, Daniel M. Zuckerman · 2021 · arXiv (Cornell University)
8. CommonNNClustering—A Python package for generic common-nearest-neighbour clustering
   Jan-Oliver Kapp-Joswig, Bettina G. Keller · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
9. The Effect of Codon Translation Rates on Cotranslational Protein Folding Mechanisms of Arbitrary Complexity
   Edward P. O’Brien · 2014 · Biophysical Journal
10. Hyperbolic periodic orbits in nongradient systems and small-noise-induced metastable transitions
    Molei Tao · 2016 · arXiv (Cornell University)
11. Volume-scaled common nearest neighbor clustering algorithm with free-energy hierarchy
    R. Gregor Weiß, Benjamin Ries, Shuzhe Wang, Sereina Riniker · 2021 · The Journal of Chemical Physics
12. Spatial Scaling
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13. The influence of N-methylation on the ansamers of an amatoxin: Gly5Sar-amanullin
    Marius T. Wenz, Simone Kosol, Guiyang Yao, Roderich D. Süßmuth, Bettina G. Keller · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
14. Estimation of binding free energies with Monte Carlo atomistic simulations and enhanced sampling
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15. Information thermodynamics of transition paths between multiple mesostates
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16. Exploring the conformational dynamics of a large molecule in solution using an external electric field: A nonequilibrium molecular dynamics simulation
    Han Wang, Christof Schütte, Giovanni Ciccotti, Luigi Delle Site · 2013 · arXiv (Cornell University)
17. Data-Driven Characterization and Acceleration of Metastable Dynamics Using Koopman Operators
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18. Germline-somatic residue synergy reshapes antibody encounter-state pathways to enhance HIV-1 recognition
    Sangita Kachhap, Yishak Bililign, Jared J. Lindenberger, Carrie Saunders, Priyamvada Acharya, Rory C. Henderson · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
19. Lost in Projection? Gaussian Filtering Recovers Hidden Conformational States
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20. Predicting probabilities of climate extremes from observations and dynamics
    Dario Lucente · 2021 · theses.fr (ABES)
21. Bio-inspired design from the bottom-up : Catalysis and Self-Assembly through Folding
    Maitane Muñoz Basagoiti · 2022
22. Unveiling the Impact of Drug-Sensitive Mutations on HIV-1 Protease Dynamics: A Molecular Dynamics Simulation Study of the T12A, L63Q, and H69N Variants
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23. Entropic Transfer Operators for Stochastic Systems
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24. Germline-somatic residue synergy reshapes antibody encounter-state pathways to enhance HIV-1 recognition
    Sangita Kachhap, Yishak Bililign, Jared J. Lindenberger, Carrie Saunders, Priyamvada Acharya, Rory C. Henderson · 2026 · eLife
25. Germline-somatic residue synergy reshapes antibody encounter-state pathways to enhance HIV-1 recognition
    Sangita Kachhap, Yishak Bililign, Jared J. Lindenberger, Carrie Saunders, Priyamvada Acharya, Rory C. Henderson · 2026 · eLife
26. π -Girsanov: A generalized method to construct Markov state models from non-equilibrium and multiensemble biased simulations
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27. A Machine-Learned Symbolic Committor for a Chemical Reaction: Isomerization in Retinal and p -Coumaric Acid
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