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Minimum System Requirements
The main purpose of the program DynaFit is to perform nonlinear least-squares regression of chemical kinetic, enzyme kinetic, or ligand-receptor binding data. The experimental data can be either initial reaction velocities in dependence on the concentration of varied species (e.g., inhibitor concentration vs. velocity), or the reaction progress curves (e.g., time vs. absorbance).
The main advantage in using the program DynaFit is in the ability to characterize the (bio)chemical reacting system in terms of symbolic, or stoichiometric, equations. For example, the ``slow, tight'' inhibition of a dissociative dimeric enzyme is described by the following text:
Monomer + Monomer <==> Enzyme : k1 k2
Enzyme + Inhibitor <==> Complex : k3 k4
Enzyme + Substrate <==> ReactiveX : k5 k6
ReactiveX --> Product + Enzyme : k7 k8
The names of chemical species ("Monomer", "Enzyme", etc.) are entirely arbitrary and can be freely chosen by the investigator.
If you publish any results obtained by using DYNAFIT, plase cite the following reference:
Kuzmic, P. (1996) Anal. Biochem. 237, 260-273.
"Program DYNAFIT for the Analysis of Enzyme Kinetic Data: Application to HIV Proteinase"
A computer program with the code name DYNAFIT was developed for fitting either the initial velocities, or the time-course of enzyme reactions, to an arbitrary molecular mechanism represented symbolically by a set of chemical equations. Seven numerical tests and five graphical tests are applied to judge the goodness of fit. Experimental data on the inhibition of the dissociative dimeric proteinase from HIV were used in four test examples. A set of initial velocities was analyzed to see if a tight-binding inhibitor could bind to the HIV proteinase monomer. Three different sets of progress curves were analyzed (i) to determine the kinetic properties of an irreversible inhibitor; (ii) to investigate the dissociation and denaturation mechanism for the protease dimer; and (iii) to investigate the inhibition mechanism for a transient inhibitor.
abstract with related references concerning the kinetics of HIV-1 protease.
The nonlinear regression module uses the Levenberg-Marquardt algorithm . The time-course of (bio)chemical reactions is computed by the numerical integration of simultaous first-order ordinary differential equations, using the Livermore Solver of ODe Systems (LSODE, ). The composition of complex mixtures at equilibrium (e.g., in the concentration jump experiment where a complex mixture is incubated prior to the addition of a reagent) is computed by solving simultaneous nonlinear algebraic equations, namely, the mass balance equations for the component species, by using the multidimensional Newton-Raphson method .
- G. A. F. Seber and C. J. Wild (1989) "Nonlinear Regression", Wiley, New York, p. 624.
- A. C. Hindmarsh (1983) "ODEPACK: a systematized collection of ODE solvers"; in Scientific Computing, ed. R. S. Stepleman et al., North Holland, Amsterdam, pp. 55--64.
- E. Kreyszig (1993) "Advanced Engineering Mathematics"; 7th ed., John Wiley, New York, p. 929.
|Minimum System Requirements|
DynaFit for Windows
- Intel® Pentium® III or Celeron® class 800 MHz or faster processor
- Microsoft Windows® XP (SP1) or 2000 (SP2)
- 128 MB RAM
- 20 MB Hard Disk Space
- Ethernet Network Interface Card required for license activation(1)
- CD/DVD-ROM drive required for software installation(2)
The Network Interface Card is used to compute a unique "Computer ID", tied to a particular DynaFit license. Essentially the "Computer ID" required for license activation is an encrypted Media Access Control (MAC address) associated with the given Network Card.
CD/DVD-ROM is not required if the software is being installed by using the downloadable installer file dynafit-install.zip.