Electrostatic potentials and solvation energies in YASARA

YASARA provides various ways to visualize electrostatic potentials (ESPs) and calculate solvation energies. They are based on two very different approaches:

•  The Particle Mesh Ewald approach (PME) uses the reciprocal space part of Ewald summation to obtain the smoothed electrostatic potential in vacuo, without singularities and short-range noise[1]. The left column of figure 1 shows the resulting long-ranged PME potentials around the enzyme SOD (superoxide dismutase), where an electropositive channel (shown in blue) leads to the active site to help capture the superoxide anions.
  
• The Poisson-Boltzmann approach (PBS) uses a customized version of the APBS program[2] to solve the Poisson-Boltzmann equation, yielding the electrostatic potential with implicit solvent and counter ions. Compared to PME, the PBS potential shows more short-range details (right column in figure 1).

• The styles Density and Points (first two rows in figure 1) visualize the ESP at each point on a grid, using either transparent or opaque dots.
• The Contour style consists of two surfaces, first a contour of the regions with a certain negative potential (red), and second a contour of the regions with a certain positive potential (blue).
  
• The Surface style is the most common one, it simply colors a surface of the protein as a function of the ESP at each surface point. Van der Waals, molecular or solvent accessible surfaces can be chosen.

• A very fast empirical approximation (fraction of a second).
• A fast PME-based boundary element approach (one second).
  
• A slow PBS-based calculation with APBS[2] (many seconds).