You can try AutoDock-Vina. Blind docking is effective only when the calculation is exhaustive. There must be large number of runs in blind docking,

If you have programs such as MOE or Discovery Studio, you can change such settings in them for better results.

Blind docking is introduced for the detection of possible binding sites and in silico solutions by using docking tools focus on the (supposed) primary binding region. Thus using receptor flexibility during docking;  "blind-docking" analysis a short distance between grid points can be identified. It is used when one get exhaustive data reported on drug tries to be formulated. Blind docking system consists of  a model of proteins and peptides and  definition of the “fitness” as an energy-like property of a given protein–peptide 

I put it through 100 runs. I mainly use it to dock small drug molecules to heme proteins.

I agree with Prateek about the use of Autodock Vina due to its better performance when several runs (>100) are required. I would only add that you can try to search for close protein homologues and check whether they have already described binding sites where your proposed ligands can compete. Then, for the higher scores you may want to try to decrease your search space to improve your results. Finally, if you are aware or you expect your protein to show some degree of conformational change, you may want to try an ensemble-based approach as in Wassman CD et al, (2013) Nat Commun 4, 1407.

Good luck!

I am developing a new version of "Quick Vina" (http://bioinformatics.oxfordjournals.org/content/31/13/2214), especially for "Blind Docking".

I'll update this thread when it is ready.

You can also try our Blind Docking server:

http://bio-hpc.ucam.edu/aquiles/

Gud mrng every one for blind docking grid size ???

I forgot to update this question.

The tool is released in 2017 under the name "QuickVina-W"

https://www.nature.com/articles/s41598-017-15571-7