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10 Template Docking
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positions for the group feature.
Figure 94: Example of a template with two groups: ring atoms
(yellow) and hydrogen donor atoms (purple). The colored spheres
indicates group centers.
If an atom matches a group definition (e.g. is a hydrogen acceptor), it will be
rewarded depending on its distance to the group centers by using the following
(Gaussian) formula for each center:
e = ω*exp(-d2/r02)
where d is the distance from the position of the atom to the center in the
group. ω is a weight (importance) factor for the template group, and r0 is a
distance parameter, specifying a characteristic distance for the template group
(when d is equal to this characteristic distance, the interaction is at e-1 ~ 36%
of its maximum value). ω and r0 can be customized for each template group.
The following strategy applies when evaluating ligands during docking: For
each atom in the ligand, score contributions from all centers in all matching
groups are taken into account, i.e. a single atom may contribute to several
centers in several groups - an atom is not restricted to the closest matching
center or a single group.
The template score is normalized: the resulting score found using the
procedure above is divided by the score of a perfectly fitting ligand (i.e. if the
template was constructed from one ligand only this ligand would have a
normalized template score of 1.0). Notice that in the docking wizard it is
possible to specify an overall normalization of the similarity score term to
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