Create a simplified input file for SpringSalad in BNGL, being able to be visualized in VCell and bnglViz
begin molecules
Nephrin(anchor0,dom11,dom22,pTyr1_2__555~0~p,pTyr1_24~0~p,linker5,pTyr36~0~p,lin_dom7)
Nck(SH3_1__0,SH3_21,SH3_32,SH23,linker__4)
end molecules
begin species
Nephrin(anchor0,dom11,dom22,pTyr1_2__555~p,pTyr1_24~p,linker5,pTyr36~p,lin_dom7) 20
Nck(SH3_1__0,SH3_21,SH3_32,SH23,linker__4) 10
end species
begin reactions
pY_SH2_binding_1: Nephrin(pTyr1_2555~p) + Nck(SH23) -> Nephrin(pTyr1_2555~p!1).Nck(SH23!1) kon 100.0 koff 100.0
pY_SH2_binding_1: Nephrin(pTyr1_2555~p) + Nck(SH23) -> Nephrin(pTyr1_2555~p!1).Nck(SH23!1) kon 100.0 koff 100.A0
end reactions
SpringSaladPy will generate a generic template for the input, that has all features (radius, diffusion, links, bond lengths) with generic numbers (e.g. 1 for all radiuses, 2 for all bond lengths), random colors and coordinates for all sites.
Create a simplified input file for SpringSalad in BNGL, being able to be visualized in VCell and bnglViz
begin molecules Nephrin(anchor0,dom11,dom22,pTyr1_2__555~0~p,pTyr1_24~0~p,linker5,pTyr36~0~p,lin_dom7) Nck(SH3_1__0,SH3_21,SH3_32,SH23,linker__4) end molecules
begin species Nephrin(anchor0,dom11,dom22,pTyr1_2__555~p,pTyr1_24~p,linker5,pTyr36~p,lin_dom7) 20 Nck(SH3_1__0,SH3_21,SH3_32,SH23,linker__4) 10 end species
begin reactions pY_SH2_binding_1: Nephrin(pTyr1_2555~p) + Nck(SH23) -> Nephrin(pTyr1_2555~p!1).Nck(SH23!1) kon 100.0 koff 100.0
pY_SH2_binding_1: Nephrin(pTyr1_2555~p) + Nck(SH23) -> Nephrin(pTyr1_2555~p!1).Nck(SH23!1) kon 100.0 koff 100.A0
end reactions
SpringSaladPy will generate a generic template for the input, that has all features (radius, diffusion, links, bond lengths) with generic numbers (e.g. 1 for all radiuses, 2 for all bond lengths), random colors and coordinates for all sites.