DOCK Blaster:Dock PDB target

DOCK Blaster has the capability to perform a docking screen starting from only a PDB code in some cases. To be eligible, the PDB code should specify a file where our scripts can automatically identify the ligand and the receptor unambiguously. In some cases, it may be necessary to specify the three letter code of the ligand so DOCK Blaster knows which HET atoms you wish to use.

If DOCK Blaster cannot identify the receptor and the ligand, you may still be able to use DOCK Blaster via the "Start from a structure" starting point. This requires that you download the PDB file and prepare it by hand, including specifying the binding site. For more information, see Prepare input.

Just because DOCK Blaster can start does not mean it will end happily. In fact, in benchmarking studies (Irwin et al., J Med Chem, 2009, in press), we found that only about 18% of the 7,755 proteins attempted produced viable-looking results using fully automated docking.