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BioMOCA Suite

By David Papke1, Reza Toghraee1, Umberto Ravaioli1, Ankit Raj1

1. University of Illinois at Urbana-Champaign

Simulates ion flow through a channel.

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Version 2.3.1 - published on 23 Oct 2009

doi:10.4231/D3DB7VP9M cite this

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    SCREENSHOT #1 SCREENSHOT #2

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Abstract

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.

Credits

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).
  • David Papke; Reza Toghraee; Umberto Ravaioli; Ankit Raj (2009), "BioMOCA Suite," http://nanohub.org/resources/BMCsuite. (DOI: 10.4231/D3DB7VP9M).

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