DOCK Blaster: Difference between revisions
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To learn more please consult the topics below. | To learn more please consult the topics below. | ||
* [[DOCK Blaster:Preliminaries | Before you begin]] | |||
* [[DOCK Blaster:Preliminaries]] | |||
* [[DOCK Blaster:Prepare Input | Prepare Input ]] | * [[DOCK Blaster:Prepare Input | Prepare Input ]] | ||
** [[DOCK Blaster:Prepare Receptor | Prepare Receptor]] | ** [[DOCK Blaster:Prepare Receptor | Prepare Receptor]] | ||
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** [[DOCK Blaster:Other Input Options | Other Input Options]] | ** [[DOCK Blaster:Other Input Options | Other Input Options]] | ||
** [[DOCK Blaster:Input Troubleshooting | Input Troubleshooting]] | ** [[DOCK Blaster:Input Troubleshooting | Input Troubleshooting]] | ||
* [[DOCK Blaster:Job Management | Job Management]] | * [[DOCK Blaster:Job Management | Job Management]] | ||
* [[DOCK Blaster:Results | Results ]] | * [[DOCK Blaster:Results | Results ]] | ||
** [[DOCK Blaster:Initial Evaluation | Initial Evaluation]] | ** [[DOCK Blaster:Initial Evaluation | Initial Evaluation]] | ||
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** [[DOCK Blaster:Large Database Docking | Large Database Docking]] | ** [[DOCK Blaster:Large Database Docking | Large Database Docking]] | ||
** [[DOCK Blaster:Custom Database | Custom Database]] | ** [[DOCK Blaster:Custom Database | Custom Database]] | ||
* [[DOCK Blaster:Acquiring Compounds | Acquire Compounds]] | |||
* [[DOCK Blaster:Test Compounds | Test Compounds]] | |||
* [[DOCK Blaster:Philosophy | Philosophy]] | * [[DOCK Blaster:Philosophy | Philosophy]] | ||
* [[DOCK Blaster:Annotations | Annotations | * [[DOCK Blaster:Annotations | Annotations ]] | ||
* [[DOCK Blaster:History | History ]] | * [[DOCK Blaster:History | History ]] | ||
* [[DOCK Blaster:Credits | Credits]] | * [[DOCK Blaster:Credits | Credits]] | ||
To cite DOCK Blaster, please reference | To cite DOCK Blaster, please reference Irwin et al., "Benchmarking Sets for Molecular Docking", manuscript in preparation. | ||
For help with DOCK Blaster, please join and write to the DOCK Blaster mailing lists | For help with DOCK Blaster, please join and write to the DOCK Blaster mailing lists | ||
Revision as of 18:32, 12 February 2009
DOCK Blaster is a free-to-use service for running docking screens, on the web at http://blaster.docking.org. **DOCK Blaster is currently in beta test, so you should contact John Irwin for access until it becomes public** To use DOCK Blaster you will need the structure of a protein target and an indication of the binding site you wish to target. There are two ways to do this:
- If your target is in the PDB, you may simply specify the PDB code, in the Parser.
- If your target is not in the PDB, or you edited a PDB file, use the Preparer.
- Upload the target in PDB format (preferred) or mol2 format
- Specify the binding site using
- a docked ligand in mol2 format (preferred) or
- "hot spots", in PDB format
- atoms of residues forming the binding site, the center of inertia of which be where you expect the ligand to go.
If you do not have a particular target in mind and are simply curious about DOCK Blaster, you may select "I'm feeling lucky", and we will pick a target for you from the PDB. To try one of the examples featured in our (forthcoming) DOCK Blaster paper, consult the sample data.
To learn more please consult the topics below.
To cite DOCK Blaster, please reference Irwin et al., "Benchmarking Sets for Molecular Docking", manuscript in preparation.
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.