Dock PDB target
About DOCK Blaster
About DOCK and ZINC
About Shoichet Lab
About UCSF Pharm Chem
How much is DOCK Blaster used?
Start with a structure
Start with a PDB code
I'm Feeling Lucky
Query a Job
Introduction to DOCK Blaster
How to prepare input
Can I trust DOCK Blaster results?
What do DOCK Blaster results mean?
How long does DOCK Blaster take?
DOCK Development Interest Group
Welcome to the DOCK Blaster Parser, where all you need is a PDB code to start docking*.
To begin, all you need is a target, as specified by a PDB code. To find a PDB code, you may use the
. Not all targets will work with our current automated protocol. For an example that works, try human thyroid receptor beta (PDB code 1N46). Or pick from among
1712 PDB structures with a ligand that appear to work reasonably well [Oct 2011]
For fun, why not try one of the protein structures that are available for which no function or ligand is known? There are four sets of these, from the four PSI structural genomics centers, as follows:
JCSG (249 structures)
MCSG (610 structures)
NESG (549 structures)
NYSGXRC (266 structures)
There are over
76,000 entries in the PDB to choose from
. A fair number of these will not work with the DOCK Blaster Parser. That is what the asterisk (*) is for in the opening line. We do not know how many will work. We think perhaps 80% will run, and that perhaps as many as 30% will yield ligands worth testing. We just don't know yet. Ask us again in 2012.
If you just can't decide and want to take your chances (not really recommended), you may click: "I'm Feeling Lucky" (below). Some
is available, but it is already out of date. Working...
1712 PDB structures with ligand that appear to work reasonably well [Oct 2011]
The aim of this experiment is :
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Terms and Conditions
Bioinformatics and Chemical Informatics Research Center
Questions, Discussion, Bug reports, Feature requests
Thank you NIGMS!