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A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

Yamagishi J, Okimoto N, Morimoto G, Taiji M - J Comput Chem (2014)

Bottom Line: The presented PB radii were optimized using results from explicit solvent simulations of the large systems.The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment.The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; Laboratory for Computational Molecular Design, Quantitative Biology Center (QBiC), RIKEN, 1-6-5 Minatojima-Minatomachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.

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Correlation between the solvation free energies of training molecules calculated by PB and explicit solvent simulations. Circles are the nonterminal residues, whereas triangles are the N- or C-terminal residues. Open marks are the residues having noncharged side-chains, whereas filled marks are those having charged side-chains. The × labels correspond to polyalanines.
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fig02: Correlation between the solvation free energies of training molecules calculated by PB and explicit solvent simulations. Circles are the nonterminal residues, whereas triangles are the N- or C-terminal residues. Open marks are the residues having noncharged side-chains, whereas filled marks are those having charged side-chains. The × labels correspond to polyalanines.

Mentions: Table2 summarizes the statistical performances of our PB and other PB methods on the training molecules. Both the low mean and low standard deviation of absolute errors for our PB indicated that our optimization of PB radii was successfully accomplished. Note that the comparisons of statistical performances on simple training molecules between our PB and other PB methods are not so meaningful in themselves; however, it is useful to identify sources of errors in the solvation free energies for large peptides. From Figure 2, we can see inaccurate solvation free energies calculated by Swanson's PB for charged molecules, as expected from the inaccuracy of the reference solvation free energies. Their inaccuracy for terminal residues suggested that PB radii for N- and C-terminal residues should be distinguished from those for nonterminal residues. In contrast, Tan's PB showed high accuracy for our training molecules; Tan's results suggested that the dependency of the solvation free energies to the box size of PBC and the net charge of the solute was less problematic for small training molecules.


A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

Yamagishi J, Okimoto N, Morimoto G, Taiji M - J Comput Chem (2014)

Correlation between the solvation free energies of training molecules calculated by PB and explicit solvent simulations. Circles are the nonterminal residues, whereas triangles are the N- or C-terminal residues. Open marks are the residues having noncharged side-chains, whereas filled marks are those having charged side-chains. The × labels correspond to polyalanines.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263261&req=5

fig02: Correlation between the solvation free energies of training molecules calculated by PB and explicit solvent simulations. Circles are the nonterminal residues, whereas triangles are the N- or C-terminal residues. Open marks are the residues having noncharged side-chains, whereas filled marks are those having charged side-chains. The × labels correspond to polyalanines.
Mentions: Table2 summarizes the statistical performances of our PB and other PB methods on the training molecules. Both the low mean and low standard deviation of absolute errors for our PB indicated that our optimization of PB radii was successfully accomplished. Note that the comparisons of statistical performances on simple training molecules between our PB and other PB methods are not so meaningful in themselves; however, it is useful to identify sources of errors in the solvation free energies for large peptides. From Figure 2, we can see inaccurate solvation free energies calculated by Swanson's PB for charged molecules, as expected from the inaccuracy of the reference solvation free energies. Their inaccuracy for terminal residues suggested that PB radii for N- and C-terminal residues should be distinguished from those for nonterminal residues. In contrast, Tan's PB showed high accuracy for our training molecules; Tan's results suggested that the dependency of the solvation free energies to the box size of PBC and the net charge of the solute was less problematic for small training molecules.

Bottom Line: The presented PB radii were optimized using results from explicit solvent simulations of the large systems.The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment.The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; Laboratory for Computational Molecular Design, Quantitative Biology Center (QBiC), RIKEN, 1-6-5 Minatojima-Minatomachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.

Show MeSH