On the utilization of energy minimization to the study of ion selectivity.
The major pitfalls in studying ion selectivity in binding site models using energy minimization based methods are examined and discussed. It is shown that the properties derived from energy minimization are strongly configuration-dependent and that the results should be interpreted with caution. It is concluded that computational studies of ion selectivity must include thermal fluctuations and entropic effects.
Haibo
H
Yu
Benoît
B
Roux
D001665:Binding Sites; D003198:Computer Simulation; D019277:Entropy; D007477:Ions / Q000737:chemistry*; D008954:Models, Biological; D011188:Potassium / Q000737:chemistry; D011487:Protein Conformation; D012964:Sodium / Q000737:chemistry; D013696:Temperature; D014867:Water / Q000737:chemistry
D007477:Ions; D014867:Water; D012964:Sodium; D011188:Potassium