Installation
Easily with
conda
Medium With
pip
Hard Way by Hand
Tutorial : Introduction and Alanine Dipeptide
Overview of MSM Construction
Alanine Dipeptide Tutorial
Tutorial : Additional Methods
Cluster your data using Ward’s algorithm and the RMSD metric
Estimate a rate matrix using SCRE
Publications
MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale
Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories
Simple few-state models reveal hidden complexity in protein folding
Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer
Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
Quantifying Hub-like Behavior in Protein Folding Networks
Native States of Fast-Folding Proteins Are Kinetic Traps
Hierarchical Nyström methods for constructing Markov state models for conformational dynamics
Quantitative comparison of alternative methods for coarse-graining biological networks
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics
How long does it take to equilibrate the unfolded state of a protein?
Persistent Topology and Metastable State in Conformational Dynamics
Atomistic Simulations of Wimley–White Pentapeptides: Sampling of Structure and Dynamics in Solution
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
Equilibrium thermodynamics and folding kinetics of a short , fast-folding , beta-hairpin
MSMBuilder Commands
msmb
ConvertDataToHDF.py
CreateAtomIndices.py
Cluster.py
Assign.py / AssignHierarchical.py
CalculateImpliedTimescales.py
PlotImpliedTimescales.py
BuildMSM.py
GetRandomConfs.py
CalculateClusterRadii.py
CalculateRMSD.py
CalculateProjectRMSD.py
CalculateTPT.py
SavePDBs.py
PCCA.py
BACE_Coarse_Graining.py
Frequently Asked Questions
What’s New
2.8 Changelog
2.6 Changelog
2.5.1 Changelog
2.5 Changelog
2.0.4 Changelog
2.0.3 Changelog
2.0.2 Changelog
2.0.1 Changelog
Contributing
Submitting a bug report
How to contribute
Time-Structure Based Independent Component Analysis (tICA)
Introduction
Selection of tICA Parameters
Understanding the tICs
Drawbacks of tICA
Calculation of Autocorrelation Functions
Maximum-Likelihood Reversible Transition Matrix
msmbuilder.MSMLib
msmbuilder.MSMLib.apply_mapping_to_assignments
msmbuilder.MSMLib.apply_mapping_to_vector
msmbuilder.MSMLib.build_msm
msmbuilder.MSMLib.ergodic_trim
msmbuilder.MSMLib.ergodic_trim_indices
msmbuilder.MSMLib.estimate_rate_matrix
msmbuilder.MSMLib.estimate_transition_matrix
msmbuilder.MSMLib.get_count_matrix_from_assignments
msmbuilder.MSMLib.get_counts_from_traj
msmbuilder.MSMLib.invert_assignments
msmbuilder.MSMLib.log_likelihood
msmbuilder.MSMLib.mle_reversible_count_matrix
msmbuilder.MSMLib.permute_mat
msmbuilder.MSMLib.renumber_states
msmbuilder.MSMLib.tarjan
msmbuilder.MSMLib.trim_states
msmbuilder.MSMLib.apply_mapping_to_assignments
msmbuilder.MSMLib.apply_mapping_to_vector
msmbuilder.MSMLib.build_msm
msmbuilder.MSMLib.ergodic_trim
msmbuilder.MSMLib.ergodic_trim_indices
msmbuilder.MSMLib.estimate_rate_matrix
msmbuilder.MSMLib.estimate_transition_matrix
msmbuilder.MSMLib.get_count_matrix_from_assignments
msmbuilder.MSMLib.get_counts_from_traj
msmbuilder.MSMLib.invert_assignments
msmbuilder.MSMLib.log_likelihood
msmbuilder.MSMLib.mle_reversible_count_matrix
msmbuilder.MSMLib.permute_mat
msmbuilder.MSMLib.renumber_states
msmbuilder.MSMLib.tarjan
msmbuilder.MSMLib.trim_states
msmbuilder.msm_analysis
msmbuilder.msm_analysis.get_eigenvectors
msmbuilder.msm_analysis.get_reversible_eigenvectors
msmbuilder.msm_analysis.get_implied_timescales
msmbuilder.msm_analysis.is_transition_matrix
msmbuilder.msm_analysis.project_observable_onto_transition_matrix
msmbuilder.msm_analysis.propagate_model
msmbuilder.msm_analysis.calc_expectation_timeseries
msmbuilder.msm_analysis.sample
msmbuilder.msm_analysis.msm_acf
msmbuilder.assigning
msmbuilder.assigning.assign_in_memory
msmbuilder.assigning.assign_with_checkpoint
msmbuilder.clustering
msmbuilder.clustering.BaseFlatClusterer
msmbuilder.clustering.Clarans
msmbuilder.clustering.Hierarchical
msmbuilder.clustering.HybridKMedoids
msmbuilder.clustering.KCenters
msmbuilder.clustering.concatenate_prep_trajectories
msmbuilder.clustering.unconcatenate_trajectory
msmbuilder.clustering.concatenate_trajectories
msmbuilder.clustering.deterministic_subsample
msmbuilder.clustering.stochastic_subsample
msmbuilder.clustering.p_norm
msmbuilder.drift
msmbuilder.drift.get_epsilon_neighborhoods
msmbuilder.drift.hitting_time
msmbuilder.drift.square_drift
msmbuilder.cfep
To Do
msmbuilder.cfep.contact_reaction_coordinate
msmbuilder.cfep.VariableCoordinate
msmbuilder.cfep.CutCoordinate
msmbuilder.SCRE
msmbuilder.SCRE.ConstructRateFromParams
msmbuilder.SCRE.ConvertTIntoK
msmbuilder.SCRE.FixEntry
msmbuilder.SCRE.GetFormat
msmbuilder.SCRE.LogLikelihood
msmbuilder.SCRE.MaximizeRateLikelihood
msmbuilder.SCRE.PlotRates
msmbuilder.reduce.tICA
msmbuilder.reduce.tICA.tICA
msmbuilder.reduce.tICA.tICA.initialize
msmbuilder.reduce.tICA.tICA.project
msmbuilder.reduce.tICA.tICA.save
msmbuilder.reduce.tICA.tICA.solve
msmbuilder.reduce.tICA.tICA.train
MSMBuilder
Docs
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msmbuilder.arglib.ensure_path_exists
msmbuilder.arglib.ensure_path_exists
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msmbuilder.arglib.
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