Bioinformatics: What are the softwares and tools used for molecular docking?

[rashidacse]

Well, the question is more generous.
Choice of molecular docking softwares/algorithms are dependent on what is your type of target, what is the real biological problem (inhibition/activation/conformation change/stability) and what the modeller want to design (does he/she wants to consider water molecules, metal ions, covalent interactions etc.,).
To conclude, please elaborate your question with an example of actual problem you want to analyze and then experts worldwide can suggest you which is the best tool/algorithm.
Meanwhile, you can try or test with tools mentioned by Keith Callenberg and Soumendranath Bhakat. Even for more you can visit XTutorials