DOCK Blaster

DOCK Blaster is a free web based molecular docking and virtual screening service, on the web at [1].

To get started, you will need the structure of the target in PDB format, and some specification of the binding site. Currently, we support one of two forms: * a) a docked ligand, which is used both as a control and indication of where to dock, in mol2 format. If you don't have a docked ligand, don't worry, you can also specify:

• b) residues making up the binding site, in PDB format. The center of interia of these atoms should be about the same place that the center of a docked molecule would be.

That's really all you need to have to get started. If you don't have a particular project in mind, you may use some DOCK Blaster::Sample_Data Sample Data to experiment with. To read more, please consult the topics below.

Before you get started

• DOCK Blaster:Preliminaries

Preparation and Docking

• DOCK Blaster:Prepare Input
  • DOCK Blaster:Prepare Receptor
  • DOCK Blaster:Prepare Ligand
  • DOCK Blaster:Other Input Options
  • DOCK Blaster:Input Troubleshooting
  • DOCK Blaster:Job Management

Understanding the Results

• DOCK Blaster:Results
  • DOCK Blaster:Initial Evaluation
  • DOCK Blaster:Results Browser
  • DOCK Blaster:Large Database Docking
  • DOCK Blaster:Custom Database
  • DOCK Blaster:Test Compounds

Other information

• DOCK Blaster:Philosophy
• DOCK Blaster:Annotations
• DOCK Blaster:History
• DOCK Blaster:Credits

How to cite DOCK Blaster. Please cite Huang, Shoichet, Irwin, "Benchmarking Sets for Molecular Docking", J Med Chem 2006, in press.

We welcome your feedback about DOCK Blaster. Please write to us at comments at docking.org.