Cardiolipin Remodeling Dynamical Simulation

"Dynamic simulation of cardiolipin remodeling: Greasing the wheels for an interpretative approach to lipidomics" Michael A. Kiebish, Rob Bell, Kui Yang, Toan Phan, Zhongdan Zhao, William Ames, Thomas N. Seyfried, Richard W. Gross, Jeffrey H. Chuang, and Xianlin Han. J. Lipid Res., doi:10.1194/jlr.M004796 (epub ahead of print, April 2010).
Java versions to run client-side (in beta)

Updated Dynamical Simulation

Technical Description

perl DynamicCLSimulation.pl -remodelingpool remodelingpool.txt -inits inits.txt -PG pg.txt -alpha 0.1 -iterations 1000 -massspec -pcpe 2 -acaPE 5 -decayRate 0.2 -sn1sn2 1
Remodeling pool file:
Initial cardiolipin file:
PG file:
alpha (e.g 0.05):
iterations (e.g. 50):
Mass Spec. output: Full chain output:
pcpe (e.g. 2):
acape (e.g. 5):
decayRate (e.g. 0.2):
sn1sn2 (e.g. 1):
Dynamical Simulation viewer (mass spec data only)

Sample remodeling pool file
Sample initial cardiolipin file
Sample pg file


Get One Frame from Updated Dynamical Simulation

Technical Description

perl DynamicCLSimulation_oneframe.pl -remodelingpool remodelingpool.txt -inits inits.txt -PG pg.txt -alpha 0.1 -iterations 1000 -massspec -pcpe 2 -acaPE 5 -decayRate 0.2 -sn1sn2 1
Remodeling pool file:
Initial cardiolipin file:
PG file:
alpha (e.g 0.05):
iterations (e.g. 50):
Mass Spec. output: Full chain output: Hybrid output:
pcpe (e.g. 2):
acape (e.g. 5):
decayRate (e.g. 0.2):
sn1sn2 (e.g. 1):

Remodeling Pool File Generation

Technical Description

perl remodelingpool.pl -pinput pinputs.txt > remodelingpool.txt
pinput file:

Sample pinput file
Sample pinput file without acyl CoA


Initial Cardiolipin File Generation

Technical Description

perl pg2cardiolipin.pl -pg pg.txt > initial_cardiolipin.txt
pg file:

Sample pg file


Get TAG equilibrium

Technical Description

perl TAGsteady.pl -FAchains FAchains.txt
FAchains file:

Sample input fatty acid chains file