(1) postoia: http://sourceforge.net/projects/pistoia

An initiative to provide an open foundation of data standards,
ontologies and web-services to streamline the Pharmaceutical Drug
Discovery workflow (Chemistry, Biological Screening, Logistics)
through common business terms, relationships and processes

(2) Molecule Master: http://sourceforge.net/projects/moleculemaster
and http://moleculemaster.sourceforge.net/

MoleculeMaster is a plugin-oriented expandable architecture for both
small and large molecule study and manipulation. It includes molecule
editors, 3D viewers, the ability to run molecular mechanics, dynamics
and docking models, among other things.

The aims of number (2) dovetail with Avogadro...

- Noel

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