The calculation of free-energy profiles in proteins, and, more specifically, in ion channels, is a challenge for modern numerical simulations due both to the convergence problems associated with the electrostatics of the environ- ment and to the difficulties in modeling the fields acting on the permeating ions. The present study aims at comparing three different simulation techniques available in the litera- ture on a nanometric channel protein chosen as a test case, with the purpose of establishing their real predictivity and limits.
Exploring free-energy profiles through ion channels: comparison on a test case
CECCARELLI, MATTEO
2007-01-01
Abstract
The calculation of free-energy profiles in proteins, and, more specifically, in ion channels, is a challenge for modern numerical simulations due both to the convergence problems associated with the electrostatics of the environ- ment and to the difficulties in modeling the fields acting on the permeating ions. The present study aims at comparing three different simulation techniques available in the litera- ture on a nanometric channel protein chosen as a test case, with the purpose of establishing their real predictivity and limits.
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