Improving the description of salt bridge strength and geometry in a Generalized Born model.
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ABSTRACT:
SUBMITTER: Shang Y
PROVIDER: S-EPMC3390179 | biostudies-literature | 2011 Feb
REPOSITORIES: biostudies-literature
Publications
Improving the description of salt bridge strength and geometry in a Generalized Born model.
Shang Yi Y Nguyen Hai H Wickstrom Lauren L Okur Asim A Simmerling Carlos C
Journal of molecular graphics & modelling 20101202 5
The Generalized Born (GB) solvent model is widely used in molecular dynamics simulations because it can be less computationally expensive and it samples conformational changes more efficiently than explicit solvent simulations. Meanwhile, great efforts have been made in the past to improve its precision and accuracy. Previous studies have shown that reducing intrinsic GB radii of some hydrogen atoms would improve AMBER GB-HCT solvent model's accuracy on salt bridges. Here we present our finding ...[more]
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