Generalized Born solvation model

Tsui V, Case DA (2001) Theory and applications of the generalized Born solvation model in macromolecular simulations, Biopolymers, 56 275-291... [Pg.334]

Tsui V, Case DA (2002) Molecular dynamic simulations of nucleic acids with a generalized born solvation model, J Am Chem Soc, 122 2489-2498... [Pg.337]

The generalized Born solvation models o " " take account of specific water interactions explicitly and give excellent agreement in the AMl-SMl and PM3-SM3 cases AMl-SMl is less successful, albeit still improved over the most reasonable BKO treatment. Cavity radii are not an issue for these models. [Pg.45]

Tsui, V., Case, D.A. Molecular dynamics simulations of nucleic adds with a Generalized Born solvation model. J. Am. Chem. Soc. 2000,122,2489-98. [Pg.120]

A.V. Marenich, C.J. Cramer, and D.G. Truhlar, Generalized Born solvation model SM12, J. Chem. Theory Comput. 9 (2013), pp. 609-620. [Pg.139]

Generalized Born Solvation Model in Macromolecular Simulations. [Pg.419]

Influence of the molecular environment on the structure and dynamics of molecular subsystems will be outlined referring to the solvation free energy (Chapter 4). Implicit solvent models based on the Poisson-Boltzmann (PB) equation and the Generalized Born (GB) model is discussed in 5 and 6. The PB or GB models are used for studies of molecular electrostatic properties and allow proper assignments of positions of protons (hydrogen atoms) within the given (bio)molecular structure. [Pg.205]

Models for which the parameterizations are based on the solvent accessible surface area (SASA) are widely known in literature.58 The nonpolar component of the free energy of solvation is described in these models as a polynomial of A , where A, is the SASA of the atom i. A very good example of such approach is the Surface Generalized Born/Nonpolar Model (SGB/NP), proposed by Gallicchio and Levy.83 The nonpolar contribution is expressed as ... [Pg.218]

Among the many approximate models for solvation free energy evaluation, the most frequently used is the generalized Born (GB) model. It evaluates the solvation energy using the following equation ... [Pg.269]

Roe, D.R., Okur, A., Wickstrom, L., Hornak, V., Simmerling, C. Secondary stmcture bias in Generalized Born solvent models Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. J. Phys. Chem. B 2007, 111, 1846-57. [Pg.120]

The need for computationally facile models for dynamical applications requires further trade-offs between accuracy and speed. Descending from the PB model down the approximations tree. Figure 7.1, one arrives at the generalized Born (GB) model that has been developed as a computationally efficient approximation to numerical solutions of the PB equation. The analytical GB method is an approximate, relative to the PB model, way to calculate the electrostatic part of the solvation free energy, AGei, see [18] for a review. The methodology has become particularly popular in MD applications [10,19-23], due to its relative simplicity and computational efficiency, compared to the more standard numerical solution of the Poisson-Boltzmann equation. [Pg.129]

The most widely used implicit solvation models in biomolecular simulations are probably the Generalized Born (GB) models [63, 79], because they are computationally inexpensive and amenable to analj ic forces. GB models posit that the electrostatic solvation energy can be expressed in the form... [Pg.382]

An entirely different approach to the treatment of electrostatic interactions is to eliminate them entirely in favor of implicit solvation techniques [28, 315] which either solve the Poisson-Boltzmann equation [144, 337] or employ the Generalized Born [291] model of excluded volumes. [Pg.406]

The generalized Born/surface area (GB/SA) model is a combination of the Born and SASA models. This method has been effective in describing the solvation of biomolecular molecules. It is incorporated in the MacroModel software package. [Pg.211]

Using a set of (partial) atomic charges is often called the generalized Born model. It can be noted that the Born model predicts equal solvation for positive and negative ions of the same size, which is not the observed behaviour in solvents like H2O. [Pg.395]

Totrov [31] developed a model to estimate electrostatic solvation transfer energy AGd" in Eq. (1) based on the Generalized Born approximation, which considers the electrostatic contribution to the free energy of solvation as ... [Pg.386]

Bashford, D. and Case, D. A. 2000. Generalized Born Models of Macromolecular Solvation Effects Annu. Rev. Phys. Chem., 51, 129. [Pg.424]

Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model. [Pg.49]

Bashford D, Case DA (2000) Generalized born models of macromolecular solvation effects, Annu Rev Phys Chem, 51 129-152... [Pg.335]

Jayaram B, Sprous D, Beveridge DL (1998) Solvation free energy of biomacromolecules parameters for a modified generalized born model consistent with the AMBER force field, J Phys Chem B, 102 9571-9576... [Pg.336]

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