In this study, chemical feature based pharmacophore models of MMP-1, MMP-8 and 
MMP-13 inhibitors have been developed with the aid of HypoGen module within 
Catalyst program package. In MMP-1 and MMP-13, all the compounds in the training 
set mapped HBA and RA, while in MMP-8, the training set mapped HBA and HY. These 
features revealed responsibility for the high molecular bioactivity, and this is 
further used as a three dimensional query to screen the knowledge based designed 
molecules. These pharmacophore models for collagenases picked up some potent and 
novel inhibitors. Subsequently, docking studies were performed for the potent 
molecules and novel hits were suggested for further studies based on the docking 
score and active site interactions in MMP-1, MMP-8 and MMP-13.