[quoted from a user enquiry]
Does your pharmacophore model include geometric constraints between functional or pharmacophore groups?
At present it is a topological model, thus geometric constraints cannot yet be included.
However, topological constraints can be added in form of a pharmacophore hypothesis
We are planning to add 3D pharmacophore fingerprints to our software in future. This will allow geometric constraints between pharmacophore points.
I would like to take the opportunity to draw your attention to some advanced features
of our pharmacophore suite:
- pharmacophore type definitions are open, user can define new properties or change the definition of existing ones;
- pharmacophore point type perception can use either rules (pattern matching) or the estimation of physico-chemical properties (pKa, charge), or a combination of these two;
- fuzzy smoothing of fingerprints can be applied to enhance the pharmacophore model;
- wide choice of dissimilarity metrics is available, and these metrics can be optimized for your set of known actives by an optimization program in order to achieve the highest possible hit ratio.
Hello, I used the Ward application to cluster a chemolibrary of about 8000 compounds. The kelley indice is 70. I'm surprise because the solution don't present any singletons... Is it normal? Do must I specify an option to obtains singletons?
The second problem is that I don't arrive to find the dendrogram of the solution... How can I obtain it?