12.11. LR CBNGL MCell Rules model

12.11.1. Description

In this example reactions between molecules with a specific number of bonds is introduced. Volume molecules L have three components r , r , r and volume molecules V have two components l and l. Volume molecules L have three components r , r and r. Volume molecules R with one unbound components can react with volume molecules L with three unbound components to form a complex with one bond (through the following equation R(l) + L(r,r,r) -> L(r!1,r,r).R(l!1)). Furthermore, volume molecules R(r) with one unbound state can react with volume molecules L(r,r,r!+) with one bound state to generate with two bound states (through the reaction R(l) + L(r,r,r!+) -> L(r!1,r,r!+).R(l!1)). Finally volume molecule L(r,r!+,r!+) with two bound states can react with one volume molecule R(l) with one unbound state to form a complex L(r!1,r!+,r!+).R(l!1) (through the reaction R(l) + L(r,r!+,r!+) -> L(r!1,r!+,r!+).R(l!1)).

12.11.2. Demonstrated features

• Definition of molecules with components and states.

• Usage of BioNetGen compartments.

• Complexes are formed.

• Usage of bound states (!+) in reactions from BioNetGen notation.