analysis of ligand binding to protein structure

 AutoDock is a prime representative of the programs addressing the
 simulation of the docking of fairly small chemical ligands to rather big
 protein receptors. Earlier versions had all flexibility in the ligands
 while the protein was kept rather ridgid. This latest version 4 also
 allows for a flexibility of selected sidechains of surface residues,
 i.e., takes the rotamers into account.
 .
 The AutoDock program performs the docking of the ligand to a set of
 grids describing the target protein. AutoGrid pre-calculates these grids.