Atomic solvation parameter

Two further energy functions based on Poisson-Boltzmann electrostatics and atomic solvation parameter (ASP)-based parameterizations of the solvation free energy changes43 were evaluated by Weng et al.57 in the context of side-chain optimization after rigid-body docking. 

ASP atomic solvation parameters, BD Brownian dynamics, DEE dead end elimination, DOF... 

Wesson L, Eisenberg D (1992) Atomic solvation parameters applied to molecular dynamics of proteins in solution, Protein Sci, 1 227-235... 

In most empirical scoring functions, a hydrophobic character is attributed to several atom types, with equivalent weight for all hydrophobic contributions. In a more sophisticated approach, the propensity of particular atom types to be solvent-exposed or embedded in the interior of a protein can be assessed by so-called atomic solvation parameters. These have been derived, for example, from experimental octanol/water partition coefficients (303, 304) or from protein crystal structures (305, 306). Atomic solvation parameters are used in the VALIDATE scoring function (307) and have been tested in DOCK (308). 

Examples of empirical descriptors can be considered to be the -+ Taillander index (restricted to substituted benzenes), - second-grade structural parameters (restricted to alkenes), - polar hydrogen factor (restricted to halogenated hydrocarbons), - hydrophobic fragmental constants, - six-position number, Idoux steric constant, -> hydrophilicity index, - adsorbability index, -> bond flexibility index, and -+ atomic solvation parameter. 

Wesson, L. and Eisenberg, D. (1992) Atomic Solvation Parameters Applied to... 

Kang, H., Choi, H. and Park, H. (2007) Prediction of molecular solvation ftee energy based on the optimization of atomic solvation parameters with genetic algorithm. /. Chem. Inf. Model., 47, 509-514. 

GB/S A Generalized-Born/Surface-Area. A method for simulating solvation implicitly, developed by W.C. Still s group at Columbia University. The solute-solvent electrostatic polarization is computed using the Generalized-Born equation. Nonpolar solvation effects such as solvent-solvent cavity formation and solute-solvent van der Waals interactions are computed using atomic solvation parameters, which are based on the solvent accessible surface area. Both water and chloroform solvation can be emulated. 

L. Wesson and D. Eisenberg, Protein Sci., 1,227 (1992). Atomic Solvation Parameters Applied... 

Corey-Pauling-Kaltun (CPK) surfaces and coloring atoms according to two coloring schemes (see tables I and II). Both the Feldmann scheme (37) and the scheme based on the Eisenberg Atomic Solvation Parameter (ASP) (38), were based on how each residue would be charged at pH 7.4. 

Coloring of atoms according to their hydrophobicity is based on D. Eisenberg s Atomic Solvation Parameter (Aa) Aa = AG/A... 

Figure 4. (A) Front view (looking into the active site) and (B) back view of human lysozyme colored according to Feldmann s functional color scheme. Front view of (C) human lysozymes colored according to Eisenberg s atomic solvation parameters. Tryptophan residues are additionally colored red. Continued on next page.

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