Affinito, F., Brunetti, R., Jacoboni, C. et al. J Comput Electron (2005) 4: 171. doi:10.1007/s10825-005-7132-7
A physical model and a simulation framework are proposed for the analysis of conduction properties of ion channels. The permeation path of ions along the channel is defined through the simultaneous occupancy of a set of individual ion binding sites within the pore identified from structural X-ray data and Molecular Dynamics (MD) simulations. All permitted elementary transitions between different channel configurations and their rate constants can be evaluated from the atomistic structure and MD data and are implemented into a statistical model which is then coded in a Monte Carlo simulator. Results for K ions permeating the KcsA channel are shown.
ion channelsKcsAmolecular dynamicsstatistical modelsMonte Carlo simulator