Create New Features and Change Feature Types
LigandScout provides three geometric types of features:
vector (H-Bond Acceptor, H-Bond Donor, Iron Binding Location,
Magnesium Binding Location, Zinc Binding Location),
point (Hydrophobic, Negative Ionizable, Positive Ionizable,
Exclusion Volume) and plane feature (Aromatic Ring).
You can create a vector feature between the
ligand and the environment by selecting an atom on ligand-side
and on environment-side. Then, choose your appropriate feature
in the menu
>
. To create a feature only on the ligand-side,
select at least one atom of the ligand. If you want to create an
aromatic ring feature, at least three atoms are needed to be
selected. If you choose more than one atom (ligand-side only),
the new feature is created on the average position of the selected
atoms. To switch the type of a feature, select a feature and go
to the menu
>
. A submenu shows which types can be chosen.
Deleting Selected Features
LigandScout's automated pharmacophore generation algorithm is
designed to create pharmacophores and
simplified pharmacophores
that are well-suited for most applications.
However, you may want to manually delete features of a
pharmacophore. Just select the features (spheres or vectors) in the
3D View
and
use the DEL key to erase the selected elements. The respective
command
>
and the
Delete
button provide the same functionality.
Overlapping
hydrogen bond donor
and
acceptor features
are depicted as half-green and half-red vectors.
Constistent with the respective feature type,
LEFT
mouse click on
the green part selects the donor and on the red part selects the
acceptor.
Increasing/Decreasing the Tolerance of Selected Features
The
>
and
,
respectively, allows you to adapt the tolerance spheres of selected
features. The commands allow one to
adapt the selectivity of pharmacophore models smoothly to
individual needs. The tolerance spheres have high impact on the
restrictivity of a model during virtual screening.
The commands in the menu
>
and
changes
the weight of specific features. The feature weight has an impact on
the pair-wise alignment of
pharmacophores. The value range is between 0 and 1, whereas a feature
weight near to 1 has more importance. The small sphere in the origin
of a feature changes its size according to the feature weight.
Mark Features as Optional
flags
the selected features which are not mandatory to find a valid
alignment (similar to the max. omitted feature action). During
the screening process, a molecule is still a valid hit when these
marked features are not matched.
Unmark Features as Optional
reverses the flag of the selected features. To switch off features,
select
Mark Features as Disabled
. These features
are not taken into account in the alignment process. To switch disabled
features on, select
Mark Features as Enabled
.
