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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2005
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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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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