Hi KNIME-cheminformatics community,
I’m trying the align-it pharmacophore generator node of the 3d-e-chem silico-it package. In principle this node can be really useful for the cheminformatics community and represent a great addition to KNIME but I encountered some oddity that would need to be clarified.
In the attached workflow (91.1 KB) I sketched 4 simple molecules, 3 of them used in the official align-it documentation to explain the pharmacophore generation process. You can see that the generated pharamacophores are different from what expected (see figures).
In general the following problem appears:
- No pure aromatic nor lipophilic features are created. Instead are generated always mixed aromatic/lipophilic features also in non-aromatic moyeties (see mol_3 figure).
- Mixed aromatic/lipophilic features center seem to not overlap with aromatic/aliphatic ring centers. May this be due to the pharmacophore points fusing process?
- No lipophilic features are created on aliphatic chains (see mol_3 and mol_4)
- A mixed aromatic/lipophilic feature appeared centered on a ring atom but not fused with the aromatic/lipophilic feature of the ring (see mol_2)
Please, can anybody comments on these behaviors?