PharmTree is a Pharmacophore classifier for biological properties of chemical compounds. It generates large dimensions of pharmacophore spaces based on small drug molecules' 3D conformations. The pharmacophore spaces can then be used for a variety of drug relational studies. PharmPhore Flex3D is now incorporated into PharmTree2.1. In addition to all of the features of PharmTree 1.1, PharmTree 2.1 will allow users to classify combinatorial libraries or other large sets of chemical compounds based on the PharmPhoreFlex3D fingerprints.

PharmTree uses the tree based classification technology to classify chemical compounds into different classes. It generates patterns for active compounds. It also relates a variety of biological properties each other.

PharmTree has a web-based interface. Users can install into their desk top PC, find their dataset and begin to "browse" the whole design process.

Currently, PharmTree comes with the following descriptor calculations: Molecular weight, cLogP, rotatable bounds, hydrogen bond donor, hydrogen bond acceptor, and finger prints based on PENGCC (link to e-chemserver PENGCC section) coding.