| Affinity |
Bulk is usually the rest of an enzyme which is not in the binding site.
Bulk atoms are atom in the bulk. They are fixed in Affinity docking calculations.
Freely movable atoms are movable atoms which are not restrained.
Grid buffer is the shortest distance from the grid edge to the atoms which the grid is supposed to enclose (freely movable atoms).
Grid spacing (resolution) is the distance between neighboring grid points.
Metropolis criterion is the criterion based on the Boltzmann factor.
Monte Carlo minimization is a combination of Monte Carlo (random) moves and energy minimization. The Monte Carlo moves are useful in getting over energy barriers, while energy minimization is for locating energy minima.
Movable atoms are atoms which can move during the calculation.
Restrain buffer is the region between freely movable atoms and bulk atoms.
Restrained atoms are movable atoms which are restrained to their original positions. These are in the restrain buffer.