Generalized Born models

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. 

Considering the success of fragment methods, which apply additive models for log P predichon, one can assume that addihve approaches may also sahsfactory work for MLP. Indeed, similar to the Generalized Born model, one can consider fragments of molecules as centers of some potenhal functions and use an empirically defined distance function ) to calculate the MLP value by ... 

Srinivasan J, Trevathan MW, Beroza P, Case DA (1999) Application of a pairwise generalized Born model to proteins and nucleic acids Inclusion of salt effects. Theor ChemAcc 101 426-434. 

Ghosh, A. Rapp, C.S. Friesner, R.A., Generalized Born model based on a surface area formulation, J. Phys. Chem. B 1998,102, 10983-10990... 

Michel, J., Taylor, R.D., Essex, J.W. Efficient generalized born models for Monte Carlo simulations. J. Chem. Theory Comput. 2006, 2, 732-9. 

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

In the Generalized Born model [2-5], the solvent is described in a extremely simplified way and there is no mutual polarization between solute and solvent. The Onsager model [6] allows for solute-solvent polarization, but the description of the cavity and of the solvent is still very crude. 

Onufriev A, Bashford D, Case DA (2004) Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins 55(2) 383-394... 

Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model. 

Onufriew A, Bashford D, Case DA (2000) Modification of Generalized Born Model Suitable for Macromolecules J. Phys. Chem. B 104 3712... 

Im WP, MS Lee, CL Brooks III (2003) Generalized born model with a simple smoothing function. J. Comput. Chem. 24 (14) 1691-1702... 

Xia B, Tsui V, Case DA, Dyson J, Wright PE (2002) Comparison of protein solution structures refined by molecular dynamics simulations in vacuum, with a generalized Born model, and with explicit water, J Biomol NMR, 22 317-331... 

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... 

We developed the Analytical Generalized Born plus Non-Polar (AGBNP) model, an implicit solvent model based on the Generalized Born model [37-40,44, 66] for the electrostatic component and on the decomposition of the nonpolar hydration-free energy into a cavity component based on the solute surface area and a solute-solvent van der Waals interaction free energy component modeled using an estimator based on the Born radius of each atom. 

The generalized Born model is given by the following equation [37],... 

The SMx Approach Generalized Born Electrostatics Augmented by First-Hydration-Shell Effects Each of the foregoing solvation models, when implemented at the semiempirical level, resembles closely its implementations employing ah initio molecular orbital theory—indeed, the ab initio versions often predate the semiempirical. On the other hand, the generalized Born model, discussed with respect to Equation [16] for the case of molecular mechanics,has certain properties that make it particularly appropriate i" to the semiempirical level. 27,202,203 Qur own SMx models, where SM denotes solvation model, take advantage of this, and we now review these models. 

Dominy BN, Brooks CL. 1999. Development of a generalized Born model parametrization for proteins and nucleic acids. J. Phys. Chem. B 103 3765-73... 

Zou, X., Sun, Y., Kuntz, I.D. Inclusion of solvation in ligand binding free energy calculations using the generalized-Born model. J. Am. Chem. Soc. 1999, 121, 8033 3. 

Liu, H.-Y., Zou, X. Electrostatics of ligand binding Parametrization of the generalized born model and comparison with the Poisson-Boltzmann approach. J. Phys. Chem. B 2006, 110,... 

In Fig. 2, the initial X-ray structure (left) is compared with the structure optimized using the generalized Born model (middle) and the explicit water model (right). The... 

Bashford D, Case DA. Generalized Born models of macromolecular solvation effects. Annu Rev Phys Chem 2000 51 129-152. 

Zhang LY, Gallicchio E, Friesner RA, Levy RM. Solvent models for protein-ligand binding comparison of implicit solvent Poisson and surface generalized Born models with explicit solvent simulations. J Comput Chem 2001 22 591-607. 

III.D) where the solute is treated quantum mechanically and the solvent molecules classically [186-197]. The second approach [185] may be implemented in an entirely classical framework (e.g., through the solution of the Poisson equation or the introduction of the generalized Born model in molecular mechanics) or in a quantum mechanical framework where the wavefunction of the solute is optimized self-con-sistently in the presence of the reaction field which represents the mutual polarization of the solute and the bulk solvent. Due to the complexity of solvation phenomena, both approaches contain a number of severe approximations, and if a quantum chemical description is employed at all, it is usually restricted to the solute molecule. When choosing such a quantum chemical description from the usual alternatives ab initio, DFT, or semiempirical methods) it should be kept in mind that ab initio or DFT calculations may provide an accuracy that is far beyond the overall accuracy of the underlying solvation model. For a balanced treatment it may be attractive to employ efficient semiempirical methods provided that they capture the essential physics of solvation. The performance and predictive power of such semiempirical solvation models may then be improved further by a specific parametrization. 

Sigalov, G., Scheffel, R, Qnufriev, A. Incorporating variable dielectric environments into the Generalized Born model. J. Chem. Phys. 2005,122. 

Formaneck, M.S., Cui, Q. The use of a Generalized Born model for the analysis of protein conformational transitions A comparative study with explicit solvent simulations for chemotaxis Y protein (CheY). J. Comput. Chem. 2006,27,1923M3. 

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