The knowledge about to which biomolecules a small molecule binds is highly valuable in the drug development process. Although analytical methods to dissect ligand-binding proteome have made substantial progress in the past decades, it is generally too costly, if not infeasible, to know where a small molecule binds at very high resolution. Computational prediction of binding partners of small chemical molecules has become a useful approach to evaluate their potential therapeutic applications or adverse effects. In this article two computational approaches that were adopted to perform target identification, namely, molecular docking and pharmacophore fitting, are reviewed. Both approaches enable the identification of key interactions between the biomolecules and the small molecules. Databases that can be used to further improve the implementation and the computational methods and to benchmark their performances are also included.