Submitted by keithc on Fri, 02/17/2012 - 14:38
UPDATE: this functionality is now built into APBSmem, our interface for electrostatics calculations on membrane proteins.
Although this functionality will be built into our APBSmem interface very soon, in this tutorial we will use a script with our draw_membrane Java tool that models the membrane as a low dielectric slab to calculate the ion solvation permeation pathway.
Submitted by keithc on Tue, 07/05/2011 - 18:05
Below are images of KcsA with and without an implicit low-dielectric membrane. All other aspects of the two systems are identical. Field lines from an APBS electrostatics calculation show the effect of the membrane on the electrostatic potential. The images more or less speak for themselves. The membrane is a significantly different environment from bulk solvent.
Submitted by keithc on Thu, 09/30/2010 - 10:32
You can read our recent paper on APBSmem published in PLoS ONE at http://www.plosone.org/article/info:doi/10.1371/journal.pone.0012722
Citation:
Callenberg KM, Choudhary OP, de Forest GL, Gohara DW, Baker NA, Grabe M. (2010) APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane. PLoS ONE 5(9): e12722. doi:10.1371/journal.pone.0012722
Submitted by keithc on Thu, 08/19/2010 - 16:20
Our paper was accepted at PLoS ONE! It will be great to have it published, particularly because we described parameters and included several case studies that we intended to provide as examples of using the software. Since we've already announced APBSmem and a good number of people are already using it, it's frustrating not being able to just send them the paper when they have questions that are answered there.
