pharmacophore of the molecule

[copied from email]





hello,





we are trying to use your API and we don't know how to get the pharmacophore of the molecule... we have the ones for the atoms but not for the molecule.


is there a java method we didn't see or must we make a method ?





thanks.





fabien cavasino & christophe clergeau

Hello Fabien & Christophe,





Our pharmacophore perception tool (PMapper) can assign pharmacophoric properties to individual atoms, but not to the molecule as a whole.





To suggest a pharmacophore model one has to consider multiple structures exhibiting the same activity (i.e. bind to the same receptor) in order to find common pharmacophore patterns shared by most active molecules.





Our tools are capable of suggesting such pharmacophore model (called pharmacophore hypothesis) but this is not a three (or four, ...) point based model, instead, a pharmacophore fingerprint that can be used in dissimalarity calculations (virtual screening).


Would this meet your needs?





The point-based pharmacophore model is among our development plans, but it is not likely to be implemented and released in near future - unless there is a strong need (and support ;-) ) for that.





Miklos