Article ID: 1492 - Last Modified: April 30, 2012
What implicit solvent model does Prime MM-GBSA use?
The SGB model in Prime MM-GBSA in Suite 2010 is based on the 1998 Ghosh/Friesner paper (http://pubs.acs.org/doi/abs/10.1021/jp982533o), but it was further parametrized as described in the following papers:
Zhu, K.; Pincus, D. L.; Zhao, S.; Friesner, R. A. Long Loop Prediction Using the Protein Local Optimization Program. Proteins: Structure, Function, and Bioinformatics 2006, 65, 438-452.
Zhu, K.; Shirts, M.; Friesner, R. Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program: Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects. J. Chem. Theor. Comput. 2007, 3, 2108-2119.
The Suite 2011 and later releases of Prime (and thus also MM-GBSA) use a further parametrized solvation model. The description of this model has been published in a paper in Proteins (wileyonlinelibrary.com, DOI: 10.1002/prot.23106).
Keywords: Prime, implicit solvent model, SGB, MM-GBSA, MMGBSA
#1484: How are Prime MM-GBSA calculations carried out, and what solvation model is used?
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