DOCK Blaster: Difference between revisions
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DOCK Blaster is a free web based molecular docking and virtual screening service, on the web at [http://blaster.docking.org]. | DOCK Blaster is a free web based molecular docking and virtual screening service, on the web at [http://blaster.docking.org http://blaster.docking.org]. | ||
To get started, you will need the structure of the target in PDB format | To get started, you will need at the very least the following: | ||
* | * The structure of the target in PDB format (best) or mol2 format | ||
* A specification of the binding site. This may be in one of two forms: | |||
** 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 intertia of these atoms should coincide with where you expect the ligand to go. | |||
That's really all you need | 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 [[DOCK Blaster::Sample_Data Sample Data]] to experiment. To read more, please consult the topics below. | ||
== Before you get started == | == Before you get started == | ||
* [[DOCK Blaster:Preliminaries]] | * [[DOCK Blaster:Preliminaries]] | ||
== Preparation and Docking == | == Preparation and Docking == | ||
| Line 16: | Line 19: | ||
** [[DOCK Blaster:Other Input Options]] | ** [[DOCK Blaster:Other Input Options]] | ||
** [[DOCK Blaster:Input Troubleshooting]] | ** [[DOCK Blaster:Input Troubleshooting]] | ||
** | ** [[DOCK Blaster:Job Management]] | ||
== Understanding the Results == | == Understanding the Results == | ||
| Line 32: | Line 35: | ||
* [[DOCK Blaster:Credits]] | * [[DOCK Blaster:Credits]] | ||
To cite DOCK Blaster, please reference Huang, Shoichet, Irwin, "Benchmarking Sets for Molecular Docking", J Med Chem 2006, 49(23), 6789-6801 | |||
We welcome your feedback about DOCK Blaster. Please write to us at comments at docking.org. | We welcome your feedback about DOCK Blaster. Please write to us at comments at docking.org. | ||
Revision as of 19:22, 5 December 2006
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 the very least the following:
- The structure of the target in PDB format (best) or mol2 format
- A specification of the binding site. This may be in one of two forms:
- 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 intertia 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 DOCK Blaster::Sample_Data 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
We welcome your feedback about DOCK Blaster. Please write to us at comments at docking.org.