Generalized Bom model

Totrov, M. Accurate and efficient generalized Bom model based on solvent accessibility derivation and application for logP octanol/water prediction and flexible peptide docking, f Comput. Chem. 2004, 25, 609-619. 

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

X. Xou, Y. Sun, and I. Kuntz, Inclusion of solvation in ligand binding free energy calculations using the generalized-Bom model, J. Am. Chem. Soc. 121 8033 (1999). 

In the generalized Bom model, the solvent polarization energy, Gpoi, is approximated by the following equation... 

The incorporation of the generalized Bom model into free energy calculation methods using FEP/TI and A-dynamics was carried out by Banba and Brooks.81 They define the electrostatic solvation energy for the hybrid system as follows... 

D. Bashford and D. A. Case, Generalized Bom models of macromolecular solvation... 

The generalized Bom model (GBM) can be regarded as a special case of the preceding procedures the reaction field is expressed in terms of a multi-center monopole representation of the solute molecule, using the Bom formula, Eq. (32).l3 ,6, 3 "5 The centers are the atomic nuclei. The results are quite sensitive to the method used to calculate the atomic charges Cramer and Truhlar, who have applied the GBM approach extensively13,16,107 use their Class IV charges for this purpose.16,107,116 Various techniques have been utilized to determine the radii.16,95,101,107... 

Kang, X. S., Shafer, R. H., and Kuntz, I. D. 2004. Calculation of Ligand-nucleic Acid Binding Free Energies with the Generalized-Bom Model in dock . Biopolymers, 73, 192. 

Generalized Bom models do not suffer from the multiple cavity problem, which is a particular advantage of that methodology. However, initial studies have suggested that... 

Liu, H. Y., and Zou, X. (2006). Electrostatics of ligand binding Parametrization of the generalized Bom model and comparison with the Poisson-Boltzmann approach. J. Phys. Chem. B 110, 9304-9313. 

Bashford D, Case DA (2000) Generalized Bom Models of Macromolecular Solvation Effects Annu. Rev. Phys. Chem. 51 129-152... 

Grycuk TJ (2003) Deficiency of the Coulomb-field approximation in the generalized Bom model, An improved formula for Bom radii evaluation. Chem. Phys. 119 4817... 

Wojciechowski M, Lesyng B (2004) Generalized Bom Model, Analysis, Refinement and Applications to Proteins, J. Phys. Chem. B 108 18368-18376... 

Using a set of (partial) atomic charges is often called the generalized Bom model. It <... 

The effect of induced dipoles in the medium adds an extra term to the molecular Hamilton operator. = -r R (16.49) where r is the dipole moment operator (i.e. the position vector). R is proportional to the molecular dipole moment, with the proportional constant depending on the radius of the originally implemented for semi-empirical methods, but has recently also been used in connection with ab initio methods." Two other widely available method, the AMl-SMx and PM3-SMX models have atomic parameters for fitting the cavity/dispersion energy (eq. (16.43)), and are specifically parameterized in connection with AMI and PM3 (Section 3.10.2). The generalized Bom model has also been used in connection with force field methods in the Generalized Bom/Surface Area (GB/SA) model. In this case the Coulomb interactions between the partial charges (eq. (2.19)) are combined... 

Using a set of (partial) atomic charges is often called the generalized Bom 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 H 0. 

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