Discover Modern Kinetics

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Enzyme Kinetics Data Fitting and Simulation

Enzyme Kinetics Workshop 4-day Intensive May 26-30, 2019

Model complexity with ease.

Complex models? 100-step polymerizations? Yes.

The example above shows the simple text entry and resulting visual model of actomyosin and myosin ATPase. Note the automatically detected thermodynamic cycle indicated in red, which can be used as a constraint in fitting. Several experiments have been set up to mimic stopped-flow fluorescence and light scattering data.

No Simplifying Approximations

The field of enzyme kinetics evolved before computers were available. In the early days, it was out of necessity that kinetic data were treated with analytic transforms such as Lineweaver-Burke. Unfortunately, many antiquated methods involving analytic solutions are in use today, despite the availability of fast computers and powerful non-linear regression software.

KinTek Explorer has an intuitive graphical interface driving powerfully optimized C++ code allowing you to accurately model experiments you have performed and plan ones you envision. Dedicated UI for multiple incubation steps, incremental titrations, series of concentrations, pH, or voltages, and short-cuts to define repeated reaction sequences hundreds of steps long - among many other domain-specific features - mean that simplifying approximations can be eliminated.

Want to see an overview in action?

See the video Introduction on the tutorials page for an overview of program features and a demonstration of setting up a model.

The example above is Actomyosin.mec and is included with more than a hundred others.
Download and explore freely at any time.

Dynamic simulation = real-time exploration.

Get to know your model.

There is nothing like real-time interactive visualization to communicate the behavior of complex systems. The above models a concentration series illustrating changes in fluorescence of the external aldimine formed upon reaction of serine with pyridoxal phosphate at the active site of tryptophan synthase. A minimal UI mode is shown, which is useful for teaching and presentations.

Dynamic Interactive Simulation

KinTek Explorer was written by former game developers to be extremely fast and fully interactive. Immediate visual feedback as rate constants and other model parameters are "dragged" with the mouse builds an intuitive understanding of the kinetics involved. Learn which parameters have the greatest impact on your model, and which ones have little or no impact and might better be eliminated. Link parameters to maintain constant ratios and explore parameter dependency, adjust pH, voltage, or solvent concentration continuously, all in real-time with immediate feedback.

Especially when fitting complex models, the ability to arrive at a good fit to data is often predicated on the difficult job of finding reasonable starting estimates of parameters. Exploring this parameter landscape interactively with continuous visual feedback before fitting is a huge advantage.

The fastest way to understand complex kinetics.

The unlicensed version of KinTek Explorer is completely free, fully functional*, and comes with over one hundred examples to get you started.

The above example is Tryp_synthase.mec, simulating results published in (1991) J.Biol.Chem. 266, 8020-8033.
Download to explore yourself.

Enzyme kinetics, protein folding, pharmacokinetics.

If you can capture it, we can fit it.

KinTek Explorer is used to model everything from enzyme mechanisms to protein folding, organic reaction mechanisms, bio-reactor systems, and pharmacodynamics. The example above models HIV reverse transcriptase binding kinetics and illustrates a global fit to data obtained from real experiments based on (1) rapid quench flow chemistry data and (2) stopped-flow fluorescence data. The two types of experiments are fit simultaneously to a single unifying model.

Mass Action Kinetics

KinTek Explorer converts your textual description of chemical reactions into differential equations based on the law of mass action. These differential equations are then integrated numerically to obtain reagent concentrations as a function of time. Reagent concentrations may then be used in user-defined mathematical expressions to model observable outputs which are plotted for display and are the basis for fitting your data.

Any process that can be modeled with such a system of differential equations may be simulated. Though our UI is dedicated to chemical kinetics, it's possible to model processes ranging from semiconductor physics to epidemiology.

Common use cases include modeling kinetic transients, steady-state kinetics, equilibrium titrations, fixed time point assays, and time-resolved spectra. Each of these kinds experiments (and more) can be fit simultaneously to a single unifying model.

Want to see your experiment modeled?

Send your confidential data in Excel or as tab-delimited text along with a detailed description of your experiment, including the starting concentrations, and a description of your model to We'll return to you a file for use in the free unlicensed version of the software, allowing you to explore all program features.

The data above provided in the file HIVRT_cycle.mec, from a paper by Kellinger and Johnson.
Download and explore this model.

Data-fitting designed for kinetic models.

Explore the landscape of your data.

All data-fitting software will report error estimates on fitted parameters, but this often does not tell the whole story and may be misleading. Overly complex models may appear to fit the data well, but sampling the parameter-space in the neighborhood of best fit values will visually illustrate whether or not the parameters are well-constrained, and if relationships exist among the parameters. KinTek Explorer includes FitSpace, which allows confidence contour analysis as well as pairwise dependency exploration.

Deep Domain Awareness

KinTek Explorer is designed by kinetics researchers with an interface to data-fitting that is tailored specifically to the domain of kinetics. All model parameters may be fitted or held fixed, and may have arbitrary boundaries set. Rate constants may be grouped such that two or more are held in constant ratio. Rate constant dependencies on temperature, voltage, and solvent concentration may also be specified.

Thermodynamic cycles in reaction mechanisms are automatically detected and may be used as fitting constraints. Arbitrary paths in a reaction mechanism may be specified and constrained to a known product of equilibrium constants to enforce a known free energy change. Data may be fit to analytic functions ahead of model creation. Scaling factors or offsets may be applied to series curves to account for capture inconsistencies. Error-surface landscape may be explored with FitSpace confidence countour analysis. Synthetic data may be generated to plan and understand the information content of experiments before spending time in the lab, or to use in teaching and learning kinetics.

Prefer to see some math?

See the video Fitting by Simulation on the tutorials page for a compelling look at the advantages over fitting solely to analytic functions.

The example above is Tryp_synthase.mec and is included with more than a hundred others.
Download and explore freely at any time.

KinTek Explorer: works with everything.

Import and export standard formats.

Though developed alongside KinTek hardware, KinTek Explorer reads and writes standard tab-delimited text files. Publication-ready postscript or presentation-suitable PNG plots may also be created as in the example above which illustrates pairwise confidence contours of parameters and distribution of residuals for a fit.

Your Data, Your Toolchain

KinTek Explorer is designed to work well with any hardware or software you may be using. If your data is columnar and can be held in an Excel spreadsheet, we can import it. Any data imported to the program is maintained in a visual Data Repository where it may be viewed, edited, assigned to experiments, or exported as text or graphical plots.

All functions of the program that produce graphical results, including all types of simulation and fitting, may be exported to text files which you can then manipulate with other software such as Python or MATLAB. Example MATLAB scripts for importing data are provided.

Any plots displayed in the software can also be output to encapsulated postcript ready for publication. These graphics files may be opened in a vector-editing tool such as Adobe Illustrator to refine formatting, though common formatting options are included. Bitmap PNG files appropriate for inclusion in presentations and websites are also produced.

We aim to be open.

KinTek Explorer is a tool that works conveniently and productively in your workflow, and makes import and export of data simple and transparent. If you need a different format, let us know.

*Import and export functionality is the only feature that requires a software license.
Explore purchase options.

SpectraFit: fit multi-wavelength spectra

Import and fit time-evolved spectra.

With the included SpectraFit feature, import multi-wavelength time-evolved spectra and fit it alongside any other kind of data. In the above example, two different absorption spectra have been imported, and are fit simultaneously with a concentration series at one wavelength to derive the spectra of the three species and the four rate constants.

Fit Direct-to-Spectra or SVD

When three-dimensional spectral data are imported to KinTek Explorer, a deconvolution is performed by singular value decomposition (SVD) resulting in amplitude vectors and abstract spectral components. These can then be fit to absorbing species amplitudes produced by the reaction model as set up by the user. Alternately, the absorbing species amplitudes may be fit directly to the total 3d spectra.

In either case, the result is the spectra and time-dependence of the individual species. As is always the case in KinTek Explorer, there is no restriction to pre-programmed models, and multiple experiments with various signals and protocols may be fit simultaneously.

Try it yourself.

SpectraFit is fully functional in the free unlicensed version with a number of spectral examples containing real data captured in laboratories, such as that shown above.

The above example is Spectra_C8-P.mec collected in the S. Fukuzumi lab (Osaka University) and published (2011) Neurochem. Int. 58, 447-457.
Download and explore today.

Want to learn more?

Watch video tutorials →

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