How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

Article Abstract:

A quantitative analysis of the performance of a finite-difference Poisson-Boltzmann implicit solvent with respect to the TIP3P explicit solvent in a range of systems of biochemical interest is presented. Results show an overall agreement between the tested implicit and explicit solvents for hydrogen-bonding/salt-bridging dimers and peptide monomers and dimers of different conformations and different lengths.

Peptides, Hydrogen bonding, Hydrogen bonds, Chemistry, Analytic, Quantitative chemical analysis, Chemical properties

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New-generation Amber united-atom force field

Article Abstract:

A new-generation Amber united-atom force field is developed for simulations involving highly demanding conformational sampling such as protein folding and protein-protein binding. The results have shown that the new united-atom force field is at least a factor of 200 more efficient than the Duan et al. all-atom force field for ab initio folding of the tested peptide.

Protein binding, Conformational analysis, Protein research

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Solvation model based on weighted solvent accessible surface area

Article Abstract:

The study was done using weighted solvent accessible surface area (WSAS) to calculate the solvation free energies for both organic and biological molecules. The results show that this technique is attractive for protein building and protein folding studies.

Biomolecules, Chemistry, Physical organic, Physical organic chemistry

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