Matt Harrington (matt at sbl.salk.edu) wrote:
: Can anyone suggest public domain software similar to KELL from Biosoft?
: Kell includes four programs (EBDA, LIGAND, KINETIC, LOWRY) for
: calculating association/dissociation rates, equilibrium studies, etc.
: Matt Harrington
: Salk Inst.
: From Biosoft's description of Kell:
:http://www.biosoft.com/biosoft/kelldos.htm
: KINETIC calculates association and dissociation rate constants using a
: weighted, non-linear, iterative,
: curve-fitting technique.
: EBDA and LIGAND are for analyzing equilibrium studies. EBDA performs the
: preliminary analysis of
: both saturation and competition studies (including conversion of dpm
: into concentrations), graphical
: transformation to give initial estimates required by LIGAND and a number
: of other data analysis functions.
: LIGAND then uses disk files created by EBDA to obtain final parameter
: estimates using weighted
: non-linear curve fitting techniques. In the current release, EBDA uses
: exact models to describe equilibrium
: data interactions which eliminates the need to use LIGAND in most cases.
: The program can handle many
: types of data including DPM and even data from non-radioligand
: experiments can be analyzed. The
: non-linear curve fitting has been developed to allow considerable
: user-control over fitting, whilst retaining
: the use of exact models. For example, model parameters can be readily
: fixed to a constant value and numeric
: limits placed on floating values to maximize the chances of successful
: convergence. LIGAND is widely
: quoted in the literature and, in KELL, it has been modified to include a
: user-friendly interface which makes
: the program simple to use. While much of its functionality has been
: built-in to EBDA, it remains the
: program of choice for sophisticated curve-fitting involving multiple
: ligands which are binding to multiple
: sites.
: With EBDA, LIGAND and KINETIC, once various models have been fitted to
: the data, the most
: appropriate model can be selected based on the results of statistical
: tests (e.g. F test, runs test).
: LOWRY is an assay analysis tool which incorporates a range of standard
: curve models, suitable for a wide
: variety of assay types. In the context of ligand-binding studies, it is
: used to calculate protein concentrations
: measured by the technique of Lowry et al (1951).
I'm not sure but maybe "gepasi" is a good tool for doing souch things.
I got a version from a simtel archiev, but it's years ago. Perhaps you
can search a home-page on the web using ALTA vista or something else.
gepasi simulate reactions, enzyme-substrate equibrillum. You can change kinetic
parameters and plot diagrams using gnuplot which is called automatically by gepasi.
gepasi is for free.
maybe this hps,
Arne
