Theory and applications of the generalized born solvation model in macromolecular simulations

By V. Tsui, David A. Case. Biopolymers, 2000

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Exploring protein native states and large‐scale conformational changes with a modified generalized born model (2004, methodology): “We begin by performing 6 MD simulations, 7-ns each, of thioredoxin, a 108-residue protein that had been used previously to test GB models.(25,34) The simulations, summarized in Table II, use the GB model based on either of the parameter sets [Eqs.”
Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap (2013, neutral): “Solvation models, that is, theoretical treatments that describe the effect of solvent range from continuum (implicit) solvent models [20-27] to explicit solvent models [28-31] and in the most sophisticated cases a quantum mechanical treatment [15,32,33] (not discussed in this article).”
Force fields for protein simulations. (2003, methodology): “Several groups have adopted this idea, using different training sets to determine the intrinsic radii and scaling factors (Hawkins et al., 1996; Jayaram et al., 1998; Dudek et al., 1998; Tsui and Case, 2000, 2001).”