potentials and solvation energies in YASARA
YASARA provides various ways to visualize
(ESPs) and calculate solvation energies. They are based on two very
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. The left column of figure 1 shows
resulting long-ranged PME potentials around the enzyme SOD (superoxide
dismutase), where an electropositive channel (shown in blue) leads to
active site to help capture the superoxide anions.
approach (PBS) uses a customized version of the APBS program
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).
Each of the two electrostatic potential types can be visualized in a
number of different ways:
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,
solvent accessible surfaces can be chosen.
Finally, solvation energies can be calculated in three different ways:
A very fast empirical approximation (fraction of a
A fast PME-based boundary element approach (one
A slow PBS-based calculation with APBS (many
R E F E R E N C E S
 Fast empirical pKa prediction by Ewald summation
Krieger E, Nielsen JE, Spronk CA, Vriend G (2006) J.Mol.Graph.Model.25,481-486
 Electrostatics of nanosystems: application to microtubules and
Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Proc.Natl.Acad.Sci.USA98, 10037-10041
Figure 1: The electrostatic
potential around superoxide dismutase, visualized using various
calculation methods and graphics styles.
Figure 2: Screen recording of
YASARA's interactive electrostatics tutorial. A higher quality version
can be watched at
YouTube, click on 'Watch in high quality' below the video. Since
YASARA creates these animations in real-time using
OpenGL, simply download the corresponding macro (GNU GPL licensed) from
the YASARA movie page to watch it in highest
resolution with up to 60 frames per second.