DOCKING SOFTWARES: AUTODOCK, GOLD & FLEX X

According to recent publication in Protein stop three docking programs are: AutoDock (27%), GOLD (15%) and Flex X (11%). Autodock is freely downloadable while the other two are commercial docking programs

AUTODOCK Proteinligand Docking Scoring functions Flexible docking

GOLD

FLEX X

empirical scoring function Search 1)Stimulated algorithm annealing 2)Genetic algorithm 3)Fragment building

Rigid docking Flexible docking and flexible docking semi-empirical semi-empirical scoring function scoring function 1)Stimulated annealing 2)Genetic algorithm 3)Fragment building 1) Geometric hashing 2)Pose clustering 3)Clique detection

AutoDock: more informative web pages than its competitors and because of its free academic license, it is a good starting point when wondering into the world of molecular docking software. FlexX:

provides better estimates of Root Mean Square Distance for compounds with correctly predicted binding mode.
Gold performs best on proteins with buried binding pockets but is terribly expensive.