Optimization of the GB/Sa solvation model for predicting the structure of surface loops in proteins

Article Abstract:

An optimization procedure is applied to the physically more rigorous solvation model, the generalized Born with surface area (GB/SA) together with the all-atom AMBER force field. There were no significant differences in performance among the 3 GB/SA studied and the differences are not very large and for certain individual loops are reversed.

Atomic force microscopy

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Density functional theory of solvation and its relation to implicit solvent models

Article Abstract:

A brief description on a density functional theory approach to solvation in molecular solvents is presented. The results reveal that the important features of water, such as the tetrahedral symmetry induced by the Hydrogen (H)-bounding network are still lacking in the generic dipolar function.

Usage, Density functionals, Density functional theory, Functions, Implicit, Implicit functions

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A coarse-grained protein-protein potential derived from an all-atom force field

Article Abstract:

A new reduced protein model which could be used to study protein-protein nonbonded interaction and represent each amino acid residue with one to three coarse grains is presented.

Models, Protein research, Amino acids, Protein-protein interactions

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