Please note that there is already a newer release: MolDB6

a free software package for creating a web-based, searchable molecular structure database

Norbert Haider, University of Vienna, 2009-2010

MolDB5R is a collection of fully functional PHP scripts for running a structure database with search options for text, functional groups, and structure/substructure/similarity. Included are also some Perl scripts for database setup and data import from an SD file. In addition to the features of the previous release (MolDB5), MolDB5R offers support for reactions, including RDF data import/export.

More detailed information is available in the documentation (see below) and in this publication:
Haider, N., Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach. Molecules, 15, 5079-5092 (2010).


For some information about the original ideas, please visit

The previous versions, MolDB4 and MolDB5, are documented at and

A demo MolDB5R database can be visited at


Since the release of the MolDB4 version of this package, several features have been added which make MolDB5R more user-friendly and more powerful. Features include:


Technical background
Using MolDB5R
Administration of MolDB5R
Appendix A (permissions and privileges)
Appendix B (configuration file settings)
Appendix C (performance tuning)

Example Links

Aurora Fine Chemicals
HDH Pharma
TMDU Chemical Biology Database
Focus Synthesis

NH, 2009-02-19; last update: 2014-08-20