ECL`

AnalyzeBindingKinetics

AnalyzeBindingKinetics[AssociationData, DissociationData]⟹Object

solves for kinetic association and dissociation rates such that the model described by 'reactions' fits the input AssociationData and DissociationData.

AnalyzeBindingKinetics[KineticData]⟹Object

fits to the trajectories in the data objects or protocol from ExperimentBioLayerInterferometry.

Details

Uses least-squares optimization to solve for the unknown kinetic rates such that the predicted trajectories from the resulting mechanism best fit the training trajectories.
Global optimization uses NMinimize, while Local optimization uses FindMinimum.
Simulated trajectories are generated during optimization using SimulateKinetics, which uses NDSolve to numerically solve the differential equations describing the reaction network.

Input

Output

Data Processing Options

Method Options Options

General Options

Method Options

Examples

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Basic Examples (3)

AnalyzeBindingKinetics populates the KineticsAnalysis field with a data object containing the relevant fields:

Given an Object[Data,BioLayerInterferometry] with association and dissociation data, AnalyzeBindingKinetics returns an Analysis Object:

Given an Object[Protocol,BioLayerInterferometry] with kinetics Data, AnalyzeBindingKinetics returns an Analysis Object:

Additional Examples (2)

Given dilution concentrations in mass/volume units, AnalyzeBindingKinetics runs without issue:

Given raw association and dissociation data, AnalyzeBindingKinetics returns an Analysis Object:

Options (24)

AnalyteDilutions (2)

Automatically resolve the dilution values:

Set the dilution values to set values:

AssociationBaselines (3)

If the specified object does not have any baseline data, finish the analysis with the raw association/dissociation data:

Specify a constant value to use as a baseline for all of the association data:

Specify a data object containing the baseline values used for the association data:

AssociationFitDomain (1)

Specify the domain to fit for the association curves:

AssociationRate (1)

Specify an initial guess for the range association rate constant (ka):

CompletelyReversibleBinding (1)

Specify if dissociation is expected to be completely reversible meaning that the signal should return to pre-association baseline levels:

DataFilterType (1)

Specify the type of function used to filter the data (options restricted to Gaussian, Mean, and Median):

DataFilterWidth (1)

Specify the width (in time units) of the window used to filter the data:

DissociationBaselines (2)

Specify a constant value to use as a baseline for all of the dissocaition data:

Specify a data object containing the baseline values used for the dissociation data:

DissociationFitDomain (1)

Specify the domain to fit for the dissociation curves:

DissociationRate (1)

Specify an initial guess for the range dissociation rate constant (kd):

ExcludeDilution (1)

Specify if a particular dilution value should be excluded in the fitting:

FitModel (1)

Set the fit model based on the expected binding stoichiometry and mechanism:

LinkMaxResponse (1)

Specify a single value should be used to fit the maximum response of each probe, or if each probe shoudl be treated individually:

MatchDissociationStart (1)

Specify if the dissociation curves should be normalized to match the last value of the matching association data:

MaxResponse (1)

Specify an initial guess for the range of maximum response (Rmax):

NormalizeAssociationStart (1)

Specify if the association curves should be normalized ot start at (0 Second, 0 Nanometer):

OptimizationOptions (1)

Specify the optimization options for a fit method:

OptimizationType (1)

Specify if the curves shoudl be fitted using Local or Global optimization:

SimultaneousFit (1)

Request that each set of association/dissociaiton data be fit individually:

Template (1)

Specify a template object to copy option sets from. User-defined options in the current function call override any options in the template:

Messages (5)

BindingKineticsMultipleAnalytes (1)

A warning is printed when multiple analytes are present in the input sample:

InvalidBindingKineticsDataType (1)

An error is thrown when the data input does not have the DataType of Kinetics:

NoBindingKineticsData (1)

An error is thrown when the input protocol does not have any data objects:

NoMolecularWeight (1)

An error is thrown when the linked molecule has no molecular weight used to convert mg/mL units:

SwappedBindingKineticsParameterGuesses (1)

An error is thrown when the initial parameter guesses are inverted (for example, max should be min and vice versa):

Last modified on Wed 17 Sep 2025 17:27:28