Permeability - Analyze Permeability Simulation

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Solution-based/Hit to Lead/Properties/Permeability

  • Solution-based/Small Molecule Lead-opt/ADME & Tox/Permeability

  • Product-based/Molecular Dynamics/WESTPA

  • Product-based/Molecular Dynamics/OpenMM

  • Task-based/Molecular Dynamics

  • Task-based/ADME & Tox Assessment

Description

The floe analyzes data generated by Permeability - Run Permeability Simulation and calculates the permeability coefficient based on the probability fluxes simulated using the Weighted Ensemble enhanced sampling strategy.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input Dataset (in): The dataset(s) to read records from

  • Required

  • Type: data_source

Outputs

Analysis Output (out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: Permeability Analysis

Floe Report (report): The title for the output floe report.

  • Required

  • Type: string

  • Default: Permeability Analysis Report

Failure Report (fail_report): Output report to generate upon failure

  • Type: string

  • Default: Permeability Analysis Failure Report

Rate Parameters

Display RED Rates (red): Whether or not to plot the permeability estimated using the Rate from Event Durations (RED) scheme (if available)

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Rate Calculation Mode (mode): How to calculate time evolution of rate estimates.

  • Required

  • Type: string

  • Default: cumulative

  • Choices: [‘cumulative’, ‘blocked’]

Window Size (window): The number of iterations that is either used as the interval for cumulative calculation or the block size for blocked calculation.

  • Required

  • Type: integer

  • Default: 1

Bayesian Bootstrap (bayesian): Apply Bayesian Bootstrap for estimating the confident regions

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Rate Evolution (evolution): Calculate the full evolution of the rate (True) or just the final value (False)

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Compartment Size Scaling Factor (compartment_size_scale): The scaling factor for the (donor) compartment size (i.e., (simulation box length - membrane width)/2).

  • Type: decimal

  • Default: 1.0

Probability Distribution Parameters

Block Size (block_size): The number of iterations to be taken average to calculate the free energy profile.

If left empty, all iterations will be used.

  • Type: integer

Miscellaneous Parameters

Rerun Analysis (rerun): Rerun analysis even if data is already present.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Cleanup (cleanup): Clean up intermediate data. The output record can still be used for resuming a simulation or analysis.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Deep Cleanup (deep_cleanup): Remove WESTPA data to save space for permeability results. WARNING: if this option is turned on, the output record cannot be used by the analysis floe.

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Trace Permeation Paths (traj): Trace the history of recycled walkers.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Log Verbosity (verbosity): verbose level

  • Type: string

  • Default: debug

  • Choices: [‘info’, ‘warning’, ‘error’, ‘debug’, ‘ddebug’]

Additional Information

Reference Permeability Coefficient (Logarithmic, Optional) (ref_perm): This can be a value determined by an experiment or determined by other methods as a reference

for comparison. The reference value should have a unit of cm/s and then converted to the log scale. An error can be included in a pair of parentheses, if available. Example input: -6.0 (0.1). Leave the parameter empty to not change it.

  • Type: string

Reference Permeability Coefficient Source (Optional) (ref_src): Source of the reference permeability coefficient, which can be the type of the experiment or

the name of the method that used to determine permeability. Leave the parameter empty to not change it.

  • Type: string

Identification Number for the Molecule (Optional) (mol_id): This can be any identification number (e.g., CHEMBL ID) associated with the molecule.

Leave the parameter empty to not change it.

  • Type: string

Molecule Name (Optional) (mol_name): The name for the molecule. Leave the parameter empty to not change it.

  • Type: string