However, the user maintains control and is able to guide each module, and if necessary modify its decisions. The hydrogen bonding sites are directional and are used to define target sites for the position of potential ligand atoms. It also substitutes heteroatoms into the skeletons to generate molecules with complementary electrostatic properties to the receptor site. User import and selection of templates into the program is provided by this module. These templates can then be used in the various modules of Sprout.
Some methods consider only a few lowest energy conformation of candidate ligands.
This is clearly a bad choice as receptor-ligand complexes are rarely bonded in the lowest energy conformation of candidate ligands. One can think about the generation of new scaffolds as searching an infinite 3D database. Thus, the chances of finding a novel structure motif are much greater. With this feature what used to take days on a single processor now takes only hours on parallel processors.