Three implicit solvent models, namely GBMVII, FACTS, and SCPISM, were evaluated for their abilities to emulate an explicit solvent environment by comparing the simulated conformational ensembles, dynamics, and electrostatic interactions of the Src SH2 domain and the Lyn kinase domain. This assessment in terms of structural features in folded proteins expands upon the use of hydration energy as ...

We assessed the relative merits of two approaches for including polarization effects in classical force fields for the sulfate anion. One of the approaches is the explicit shell model for atomic polarization and the other is an implicit dielectric continuum representation of the electronic polarization, wherein the polarizability density is spatially uniform. Both the solvation and ion associat...

Current methods for building models using implicit volume techniques present problems defining accurate and controllable blend shapes between implicit primitives. We present new methods to extend the freedom and controllability of implicit volume modeling. The main idea is to use a free-form curve to define the profile of the blend region between implicit primitives. The use of a free-form impl...

     In this study, the effect of the secondary structure of the protein on the acid strength of three structures of random (R), alpha helix (α) and beta sheet (b) were investigated theoretically. These structures are related to the cationic amino acids of histidine and lysine in the polypeptide chain of eight-glycine residue. Computational methods at the HF, B3LYP, X3LYP and M05-2X levels in t...

The Poisson-Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce t...

Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate so...