This paper gives an overview of computer assisted molecule design using quantitative structure activity relationships (QSAR). In deriving a QSAR for a set of compounds, one should be aware of possible properties one can use to correlate with the activity of this set of compounds. The paper describes some of the traditional and also more recently used properties that can be calculated. The traditionally used properties have been those calculated for the substituent groups that were varied on a particular scaffold, whereas the more recently used properties are those calculated on the molecule as a whole. One of the most recently used properties for comparative purposes are fields around the molecules. The technique is termed comparative molecular field analysis (CoMFA). The statistical techniques used to correlate the properties with the activity are also described and, finally, a case study is described. The case study shows the application of traditional and 3D QSAR (CoMFA) techniques on some photosystem II inhibitors.