In this presentation, I describe how to use the online BioMOCA Suite. I explain how to prepare the .pqr input protein structure from a .pdb structure. I then explain in detail how to use each of the four subtools in the BioMOCA Suite.
I do not cover in detail how the BioMOCA code works. If you are interested in learning about the code in more detail, you should watch the presentation "Ion Channels and BioMOCA" by Reza Toghraee.
The following paper also describes the BioMOCA Code:
T.A. Van 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).
Researchers should cite this work as follows:
David Papke (2008), "Practical Introduction to the BioMOCA Suite," https://nanohub.org/resources/4403.