Entering edit mode
12.8 years ago
Egon Willighagen
5.4k
Eric Martz was wondering on the Jmol mailing list if there are animations around of 3D conformational changes of protein structures due to changes in the pH?
I spent some time looking through the literature to try and answer this, because I found it pretty interesting, but I found very little. I looked through a bunch of papers on constant pH charmm simulations, but none provided movies. It seems like only one in 10 or 20 MD papers do anyway.
You can have a look at ion channels simulations and normal modes analysis. Specially acid sensing ion channels, activated by protons.