What's New in LigandScout 3?
New features introduced to LigandScout 3:
Tautomeric rearrangements
of a molecule lead to
distinct equilibrated structural states of the same chemical
compound and thus have an influence on nearly all aspects of computer-based chemical data processing. Especially for
structure-based pharmacophore modeling of ligand-protein complexes, tautomeric rearrangements are crucial for
the presence or absence of possible H-bonding interactions due to changing H-donor/H-acceptor properties.
LigandScout provides a rule-based ligand-side tautomer enumeration and ranking procedure that considers both
geometrical constraints imposed by the conformation of the bound ligand as well as intra- and inter-molecular
energetic contributions.
LigandScout provides a full fledged, test-suite conforming MMFF94 implementation for the energy calculation
and geometry optimization of molecular structures. You can calculate the strain energy of compounds in a database, energy-minimize
the structure of free molecules or optimize ligands within a binding pocket. The
parameters of the MMFF94 force field
can be customized.
For instance, you can define which components of the force field have to be considered and specify parameters for several
interactions (e.g. distance cutoffs for Van der Waals and electrostatic interactions). During a structure optimization process,
SMARTS pattern defined parts of the ligand or molecular environment can be kept fixed.
The “
right
” ligand conformation is a prerequisite for an energetically
favorable interaction with the
target receptor. Thus, consideration of multiple ligand conformations can increase significantly the quality and
reliability of derived pharmacophore models. LigandScout enables the creation of ligand-based pharmacophores from
single and multiple ligand conformations. Conformations are generated by OMEGA which can be
customized
freely to yield
optimal results.
One of the crucial parts of ligand-based pharmacophore creation is the choice of ligands
for the Training-Set and Test-Set. LigandScout offers clustering methods to assist
your decision. This functionality groups ligands according to their similarity to
each other using
distance calculation methods
.
