Ion site prediction in YASARA
YASARA Structure can predict binding sites for
metal ions in protein structures and other molecules. The approach
works by putting a fine grid over the protein and summing up the
binding contribution of surrounding oxygen atoms at each grid point,
considering ion specific parameters[1,2]. Grid points that exceed a
certain threshold are shown in green (weak binding) to white (very
The example on the right side shows predicted
Ca++ binding sites in PDB file 2F3Y (Calmodulin). Four Ca++
are found, marked with yellow arrows. These match the actual calcium
binding sites exactly (shown below).
The approach works best with divalent ions like
Ca++ or Mg++, which exhibit a stronger signal
than monovalent ions like K+ . The potential involvement
nitrogen and sulfur atoms (histidine, cysteine) is not considered yet.
R E F E R E N C E S