Logo Division of Drug Synthesis
Department of Pharmaceutical Chemistry
Faculty of Life Sciences, University of Vienna
Logo Uni Wien


Initially as a spin-off of the PharmXplorer project, cheminformatics software development has become another major field of activity in the department. A unique program, checkmol, was written in order to automatically identify chemical functional groups in 2D and 3D structure files. Currently, more than 200 functional groups are recognized by the program which has been published under the terms of the GPL (GNU General Public License). Based on checkmol’s ability to assign functional groups, a novel “chemical ontology” was recently proposed by the Blueprint Initiative at Toronto/Canada, the maintainers of the well-known Small-Molecule Interaction Database.

Extending checkmol’s functionality, the matchmol program has been developed which provides full structure/substructure search capabilities to any standard PC-based web server. Taking advantage of our program’s functionality, performance and free availability, collaboration partners (also from industry, like Bayer Business Services, Leverkusen/Germany) are implementing add-ons for popular relational database management systems such as PostgreSQL (http://pgfoundry.org/projects/pgchem/).

Based on the functionality of checkmol/matchmol, a fully functional software package for running a web-based structure database was developed: MolDB, its current version is MolDB5 (http://merian.pch.univie.ac.at/~nhaider/cheminf/moldb5.html). Features are: structure/substructure/similarity search, functional group search, text search; searches can span multiple data collections; imort/export via SDF files). The package comes with an administration back-end, it is written in PHP and contains command-line utilities for setup and maintainance (written in Perl).

Further cheminformatics activities are devoted to the creation of software tools for handling spectroscopic data, especially in the standardized JCAMP-DX format. A freely available (open-source) JCAMP-DX spectra viewer, JDXview, was developed at our department and is now referenced by the IUPAC website.