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Publications by John D. Chodera

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

PLoS Computational Biology
Molecular NeuroscienceEvolutionEcologyGeneticsBehaviorMolecular BiologySystematicsSimulationCellularComputational TheoryMathematicsModeling
2016English

Markov Models of Functional Dynamics of Histone Lysine Methyltransferases by Millisecond-Timescale Molecular Simulation and Chemical Probing

Biophysical Journal
Biophysics
2019English

Can We Automatically Detect Biologically Relevant Order Parameters in Molecular Simulation? Comparing Long Timescale Simulations of Multiple Kinases

Biophysical Journal
Biophysics
2017English

Binding Thermodynamics of Host-Guest Systems With SMIRNOFF99Frosst 1.0.5 From the Open Force Field Initiative

Journal of Chemical Theory and Computation
Theoretical ChemistryComputer Science ApplicationsPhysical
2019English

Probability Distributions of Molecular Observables Computed From Markov Models. II. Uncertainties in Observables and Their Time-Evolution

Journal of Chemical Physics
MedicineTheoretical ChemistryAstronomyPhysicsPhysical
2010English

Optimal Use of Data in Parallel Tempering Simulations for the Construction of Discrete-State Markov Models of Biomolecular Dynamics

Journal of Chemical Physics
MedicineTheoretical ChemistryAstronomyPhysicsPhysical
2011English

Bayesian Analysis of Isothermal Titration Calorimetry for Binding Thermodynamics

PLoS ONE
Multidisciplinary
2018English

Systematic Improvement of a Classical Molecular Model of Water

Journal of Physical Chemistry B
SurfacesTheoretical ChemistryMaterials ChemistryFilmsMedicineCoatingsPhysical
2013English

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