Accelerated Poisson–Boltzmann calculations for static and dynamic systems

By Ray Luo, Laurent David, Michael K. Gilson. Journal of Computational Chemistry, 2002

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Recent Developments and Applications of the MMPBSA Method (2018, positive): “…equation (PBE) (Warwicker and Watson, 1982; Bashford and Karplus, 1990; Jeancharles et al., 1991; Gilson, 1995; Edinger et al., 1997; Luo et al., 1997, 2002; Lu and Luo, 2003; Tan et al., 2006; Cai et al., 2009, 2010, 2011; Wang et al., 2009, 2010, 2012, 2013; Ye et al., 2009,…”
An overview of the Amber biomolecular simulation package (2013, methodology): “Amber v10 and onward now offers support for calculating the reaction ﬁeld and nonbonded interactions using a numerical Poisson–Boltzmann (PB) solver 35–37 as an alternative continuum solvent model.”
Exploring protein native states and large‐scale conformational changes with a modified generalized born model (2004, methodology): “Figure 1 also illustrates the source of sensitivity of large effective radii to subtle conformational changes in the GBHCT model based on Eq. (4): For approaching Fig. 1. Graphical representation of different mathematical expressions used to compute effective radius from the scaled volume integral .”
Force fields for protein simulations. (2003, background): “Second, it is difficult, although not impossible, to calculate the energy gradients that are needed for molecular mechanics (Sharp, 1991; Gilson et al., 1995; Cortis et al., 1996; Ripoll et al., 1996; Luo et al., 2002).”