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

Norbert Haider, University of Vienna, 2014

These instructions explain how to set up MolDB6 as a web-based, fully searchable molecular structure database. Structures and data can be added via a web interface or by import from an MDL SD file (at the server command-line). This import option is shown by an example (see below), using the SD files which are freely available from the PubChem FTP site at Analogously, reactions and data can be imported from an MDL RD file.

For some information about the original ideas, please visit

The previous version, MolDB5R, is documented at

MolDB6 is a collection of fully functional PHP scripts for running a structure/reaction database with search options for text, functional groups, and structure/substructure. Included are also some Perl scripts for database setup and data import/export from/to an SD or RD file.



New features in MolDB6 as compared to MolDB5R:


Technical background
Using MolDB6
Administration of MolDB6
Appendix A (permissions and privileges)
Appendix B (configuration file settings)
Appendix C (performance tuning)

NH, 2014-08-20; last update: 2014-08-20