Magnet is a program for filtering docking results to select those ligands and/or poses which make specified interactions with the target protein. Magnet is a rule based expert system which applies specific knowledge about a target system. In contrast, normal docking scoring functions can be viewed as encapsulating general knowledge about ligand-protein complexes in general. Thus, Magnet can be used in place of or in combination with existing scoring functions.
The Magnet methodology was developed by Hanneke Jansen and Eric Martin at Chiron. The Metaphorics version of Magnet has been developed by Metaphorics in collaboration with Chiron and is a complete reimplementation of the method. This version uses Metaphorics and Daylight toolkits to provide structure handling and rule matching. Magnet works well with DockIt as it shares the same data formats. However, it is possible to use Magnet with other docking programs via supplied format conversion tools.
To use Magnet, it is necessary to provide a set of rules which specify the particular interactions and other features required or desired for good ligands for the target protein. The rules (in the SEA language) can specify protein features (like residue numbers and chain names) combined with chemical substructures specified using SMARTS. A tutorial example is included in the distribution to help new Magnet users get started quickly.