 %  DOQCS : http://doqcs.ncbs.res.in/ 
 %  Accession Name = CDK2-CyclinA_activation_pathway 
 %  Accession Number = 42 
 %  Transcriber = Sharat J. Vayttaden, NCBS 
 %  Developer = May C. Morris, Claire Gondeau, John A. Tainer, and Gilles Divita 
 %  Species = Human, Xenopus 
 %  Tissue = Expressed in E.coli 
 %  Cell Compartment = Cytosol 
 %  Notes =  In this version of the CDK2/Cyclin A complex activation there is discrepancy in the first curve which plots the binding reaction of CDK2 and Cyclin A expressed in E. coli. With the published rate constants the simulation does not match the published graph (Fig.1B) in <a href = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11959850 >Morris MC. et al. J Biol Chem. (2002) 277(26):23847-53</a>. 
 
   % Note: All the concentrations are in micro Mole (uM)

function moose_convert
%Matlab simulation for chemical kinetics

% Saved on Wed Feb  2 16:28:11 2005

% Automatically generated from kkit model in MOOSE by conv_matlab

global buff;
tspan=[0, 12];
% Molecule names
molnames = {
'1 /kinetics/CDK2cycA'
'2 /kinetics/CyclinA'
'3 /kinetics/Cdk2'
'4 /kinetics/CDK2cycA*'
'5 /kinetics/basal_fluorescence'
};

bufnames = {
};

sumtotnames = {
'1 /kinetics/total_fluorescence'
};

% Initial concs of 5 molecules
y0(1) = 0;
y0(2) = 0.400007;
y0(3) = 0.1;
y0(4) = 0;
y0(5) = 1.21211;
% Sumtotal eqn for /kinetics/total_fluorescence: sumtot(1) =  (y(1) + y(4) + y(5) )
% Call the ODE solver and display results
[t, y] = ode23s(@f, tspan, y0);

hold on;
plot(t, (y(:,1) + y(:,4) + y(:,5) ));
% Evaluation function
function dydt = f(t, y)
global buff;
dydt = [
 - 0.813 * y(1) + 0.557 * y(4) + 18.9999 * y(3) * y(2) - 25 * y(1)
 - 18.9999 * y(3) * y(2) + 25 * y(1)
 - 18.9999 * y(3) * y(2) + 25 * y(1)
 + 0.813 * y(1) - 0.557 * y(4)
0
];

% end of model
