By means of virtual screening of small molecules databases it is possible to identify new potential inhibitors against a target of interest. Molecular docking is a computer simulation procedure to predict the conformation of a receptor-ligand complex. Each docking program makes use of one or more specific search algorithms, which are the methods used to predict the possible conformations of a binary complex. In the present review we describe several molecular-docking search algorithms, and the programs which apply such methodologies. We also discuss how virtual screening can be optimized, describing methods that may increase accuracy of the simulation process, with relatively fast docking algorithms.