DOCK Blaster: Difference between revisions
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== Preparation and Docking == | == Preparation and Docking == | ||
* [[DOCK Blaster:Prepare Input]] | * [[DOCK Blaster:Prepare Input | Prepare Input ]] | ||
** [[DOCK Blaster:Prepare Receptor]] | ** [[DOCK Blaster:Prepare Receptor | Prepare Receptor]] | ||
** [[DOCK Blaster:Prepare Ligand]] | ** [[DOCK Blaster:Prepare Ligand | Prepare Ligand]] | ||
** [[DOCK Blaster:Other Input Options]] | ** [[DOCK Blaster:Other Input Options | Other Input Options]] | ||
** [[DOCK Blaster:Input Troubleshooting]] | ** [[DOCK Blaster:Input Troubleshooting | Input Troubleshooting]] | ||
* [[DOCK Blaster:Job Management]] | * [[DOCK Blaster:Job Management | Job Management]] | ||
== Understanding the Results == | == Understanding the Results == | ||
* [[DOCK Blaster:Results]] | * [[DOCK Blaster:Results | Results ]] | ||
** [[DOCK Blaster:Initial Evaluation]] | ** [[DOCK Blaster:Initial Evaluation | Initial Evaluation]] | ||
** [[DOCK Blaster:Results Browser]] | ** [[DOCK Blaster:Results Browser | Results Browser]] | ||
** [[DOCK Blaster:Large Database Docking]] | ** [[DOCK Blaster:Large Database Docking | Large Database Docking]] | ||
** [[DOCK Blaster:Custom Database]] | ** [[DOCK Blaster:Custom Database | Custom Database]] | ||
** [[DOCK Blaster:Test Compounds]] | ** [[DOCK Blaster:Test Compounds | Test Compounds]] | ||
== Other information == | == Other information == | ||
* [[DOCK Blaster:Philosophy]] | * [[DOCK Blaster:Philosophy | Philosophy]] | ||
* [[DOCK Blaster:Annotations]] | * [[DOCK Blaster:Annotations | Annotations ]] | ||
* [[DOCK Blaster:History]] | * [[DOCK Blaster:History | History ]] | ||
* [[DOCK Blaster:Credits]] | * [[DOCK Blaster:Credits | Credits]] | ||
* [[Terms And Conditions]] | * [[Terms And Conditions]] | ||
* [[Just Watching]] | * [[Just Watching]] | ||
Revision as of 04:25, 2 October 2007
DOCK Blaster is a free web based molecular docking and virtual screening service, on the web at http://blaster.docking.org. To get started, you will need at least:
- The structure of the target in PDB format (preferred) or mol2 format
- A specification of the binding site, which may be one of:
- A docked ligand in mol2 format, which is also used to test the docking parameterization
- "hot spots", in PDB format, which may be based on one or more ligands.
- Atoms of residues forming the binding site. The center of inertia of these atoms should coincide with where you expect the ligand to go.
That's really all you need to get started. If you don't have a particular project in mind, and you are just curious about DOCK Blaster, you may use some sample data to experiment. To read more, please consult the topics below.
Before you get started
Preparation and Docking
Understanding the Results
Other information
To cite DOCK Blaster, please reference Huang, Shoichet, Irwin, "Benchmarking Sets for Molecular Docking", J Med Chem 2006, 49(23), 6789-6801
For help with DOCK Blaster, please join and write to the DOCK Blaster mailing lists [1]. We welcome your feedback about DOCK Blaster. Please send bug reports to support at docking.org. Please send opinions to comments at docking.org.