% MAPK cascade in solution (no scaffold)
%
% adapted from:
% http://www-aig.jpl.nasa.gov/public/mls/cellerator/notebooks/MAPK-in-solution.html
% by Sylvain Soliman <Sylvain.Soliman@inria.fr>
% Nov. 26, 2003
%
% original source:
% Levchenko, A., Bruck, J., Sternberg, P.W. (2000) .Scaffold proteins may
% biphasically affect the levels of mitogen- activated protein kinase
% signaling and reduce its threshold properties. Proc. Natl. Acad. Sci. USA
% 97( 11):5818-5823.  http://www.pnas.org/cgi/content/abstract/97/11/5818

declare MEK~parts_of({p1,p2}).
declare MAPK~parts_of({p1,p2}).

(1*[RAF]*[RAFK],0.4*[RAF-RAFK]) for RAF + RAFK <=> RAF-RAFK.

(0.5*[RAF~{p1}]*[RAFPH],0.5*[RAF~{p1}-RAFPH]) for RAF~{p1} + RAFPH <=> RAF~{p1}-RAFPH.

(3.3*[MEK~$P]*[RAF~{p1}],0.42*[MEK~$P-RAF~{p1}]) for MEK~$P + RAF~{p1} <=> MEK~$P-RAF~{p1}
   where p2 not in $P.

(10*[MEKPH]*[MEK~{p1}~$P],0.8*[MEK~{p1}~$P-MEKPH]) for MEKPH + MEK~{p1}~$P <=> MEK~{p1}~$P-MEKPH.

(20*[MAPK~$P]*[MEK~{p1,p2}],0.7*[MAPK~$P-MEK~{p1,p2}]) for MAPK~$P + MEK~{p1,p2} <=> MAPK~$P-MEK~{p1,p2}
   where p2 not in $P.

(5*[MAPKPH]*[MAPK~{p1}~$P],0.4*[MAPK~{p1}~$P-MAPKPH]) for MAPKPH + MAPK~{p1}~$P <=> MAPK~{p1}~$P-MAPKPH.


0.1*[RAF-RAFK] for RAF-RAFK => RAFK + RAF~{p1}.

0.1*[RAF~{p1}-RAFPH] for RAF~{p1}-RAFPH => RAF + RAFPH.

0.1*[MEK~{p1}-RAF~{p1}] for MEK~{p1}-RAF~{p1} => MEK~{p1,p2} + RAF~{p1}.
0.1*[MEK-RAF~{p1}] for MEK-RAF~{p1} => MEK~{p1} + RAF~{p1}.

0.1*[MEK~{p1}-MEKPH] for MEK~{p1}-MEKPH => MEK + MEKPH.
0.1*[MEK~{p1,p2}-MEKPH] for MEK~{p1,p2}-MEKPH => MEK~{p1} + MEKPH.

0.1*[MAPK-MEK~{p1,p2}] for MAPK-MEK~{p1,p2} => MAPK~{p1} + MEK~{p1,p2}.
0.1*[MAPK~{p1}-MEK~{p1,p2}] for MAPK~{p1}-MEK~{p1,p2} => MAPK~{p1,p2} + MEK~{p1,p2}.

0.1*[MAPK~{p1}-MAPKPH] for MAPK~{p1}-MAPKPH => MAPK + MAPKPH.
0.1*[MAPK~{p1,p2}-MAPKPH] for MAPK~{p1,p2}-MAPKPH => MAPK~{p1} + MAPKPH.


present(MAPK,0.3).
present(MAPKPH,0.3).
present(MEK,0.2).
present(MEKPH,0.2).
present(RAF,0.4).
present(RAFK,0.1).
present(RAFPH,0.3).

%same as 'make_absent_not_present.'
absent({?-?,?~{p1}~?}).