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The BioMOCA Suite can perform ion channel flow simulations on any user supplied channel. The suite includes: a map generator subtool, which produces protein maps for BioMOCA from the supplied PQR file; a lipid wrapper subtool, which allows the user to embed their channel in a membrane; and the boundary force potential calculator, which determines the potential energy barrier presented by the channel. The user can also download the acc and charge files produced by the map generator and lipid wrapper.
Finally, the suite contains the biology Monte Carlo simulator, which simulates ion channel flow through the user provided channel. The user has the ability to change a number of parameters, including the transmembrane voltage, intra- and extra-cellular concentrations of Na+, Cl-, K+, Ca2+, and Mg2+, and the run time.
A sample PQR file (of the gramicidin channel) can be downloaded to the right in the supporting documents section. Additionally, in the related resources secion below you can find a presentation on how the BioMOCA code works, as well as a practical guide explaining how to use the BioMOCA Suite.
Computational Electronics Group, University of Illinois at Urbanca-Champign. This work is funded by the NSF.
Cite this work
Researchers should cite this work as follows:
- T.A. Vad Der Straaten, G. Kathawala, A. Trellakis, R.S. Eisenberg, and U. Ravaioli, "BioMOCA - a Boltzmann transport Monte Carlo model for ion channel simulations," Molecular Simulatin, Vol. 31, No. 2-3, pp 151-171 (2005).