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Scatchard Analysis and MacLigand and /or PC equivalent...

Petr Kuzmic pkuzmic at biokin.com
Mon Sep 8 12:35:20 EST 1997


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.shtml
http://www.biokin.com/dynafit/tutorial/nuclease.shtml
http://www.biokin.com/dynafit/tutorial/nonspec.shtml

------------------------+------------------------
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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