Kenneth Grandchamp wrote:
> We would like to know if there is a modern version of
> MACLIGAND so as to do a SCATCHARD analysis.
>> Does anyone know if there is a PC equivalent that allows
> the same analysis ?
Equilibrium binding data following any arbitrary mechanism
(stoichiometry) can be analyzed by using the program DYNAFIT [P. Kuzmic
(1996) Anal. Biochem. 237, 260-273]. The program is available as a
freeware from BioKin Consulting.
An example problem distributed with DYNAFIT describes the binding of a
trimeric protein P (the enzyme nuclease) to DNA at two different sites.
The analysis is performed by using a 'script' file, where the binding
mechanism is described as follows:
[mechanism]
P + P + P <=> T : K(tri) equil
T + D <==> TD : K(1) equil
TD + T <==> T2D : K(2) equil
The machine then automatically constructs the mathematical model for the
bindind data and gives back the best-fit values of the equilibrium
constants (here, K(tri), K(1), and K(2). Another relevant example
describes two-site cooperative binding in the presence of non-specific
interactions:
[mechanism]
L + R <==> LR : K1 equil
L + LR <==> L2R : K2 equil
L + N <==> LN : Kn equil ; nonspecific!
The program runs on the PC, Macintosh, and several Unix platforms.
LINKS:
http://www.biokin.com/http://www.biokin.com/dynafit/index.shtmlhttp://www.biokin.com/dynafit/tutorial/nuclease.shtmlhttp://www.biokin.com/dynafit/tutorial/nonspec.shtml
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Petr Kuzmic, Ph.D. | (608) 256-4790
BioKin Consulting | fax (708) 256-1269
P.O. Box 8336 | pkuzmic at biokin.com
Madison WI 53708 | http://www.biokin.com
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