Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

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H++: a server for estimating pKas and adding missing hydrogens to macromolecules (2005, methodology): “Here, C max = 17 is used: in tests on 600 representative proteins (35), we found (J. Myers, G. Grothaus and A. Onufriev, manuscript submitted) that C max = 17 resulted in average errors of 0.2 p K units, compared with a standard treatment based upon a Monte Carlo approach (16).”
Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing (2010, methodology): “• Method 2: a more physically accurate implicit representation of water using a Generalized Born model [12, 8].”
The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling (2011, background): “…fitting generalized Born models to Poisson–Boltzmann (PB) results (note that the PB model itself has to be parameterized in some fashion),20,21 exploring performance in the folding of small proteins,22,23 and comparisons with explicit solvent simulations.24 ,25 The present work is…”