|
|
(9 intermediate revisions by the same user not shown) |
Line 1: |
Line 1: |
| [[Image:Dblogo.png|thumb|right|DOCK Blaster]]
| | DOCK Blaster is a program that does automatic docking. |
|
| |
|
| DOCK Blaster is a free service for running docking screens, on the web at [http://blaster.docking.org http://blaster.docking.org]. DOCK Blaster was developed in the [[Shoichet Lab]] at [[UCSF]] during the years 2000-2009. The service became public in August 2009, and a paper was published in J Med Chem in September 2009. The current version is 1.0.1. | | The first version of DOCK Blaster appeared in 2009. Please see [https://wiki.docking.org/index.php/Category:DOCK_Blaster Category:DOCK_Blaster] |
|
| |
|
| = What you need to start =
| | A re-write of the idea of DOCK Blaster, blastermaster.py, was part of the [[DOCK 3.7]] release in 2012. |
| To use DOCK Blaster you will need the structure of a protein target and an indication of the binding site. There are three ways to do this:
| |
|
| |
|
| * If your target is in the PDB, you may simply specify the PDB code, in the [http://blaster.docking.org/parser.shtml Parser]. | | In 2022 there were major developments. First, we reorganized the DOCK repo into three repos: |
| | * dock3 - the fortran source code and not much else |
| | * pydock3 - all the scripts to run docking except for 3d ligand building |
| | * ligdock3 - 3d ligand building pipeline |
|
| |
|
| {{TOCright}}
| | There is also |
| | * cheminftools - various tools. |
|
| |
|
| * If your target is not in the PDB, or you edited a PDB file, use the [http://blaster.docking.org/start.shtml Preparer]. The steps are:
| | DOCK is distributed via the dock license server dock.compbio.ucsf.edu where it is licensed for free to academics and for a small fee to companies. |
| ** 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 should be where you expect the ligand to go.
| |
| ** Click "DOCK" and wait for the job to run (typically under 1 hour).
| |
|
| |
|
| * 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.
| | The name of all the software together is "UCSF DOCK" and the current version is 3.8.1.0.0, so "UCSF DOCK 3.8.1.0.0" |
|
| |
|
| To try one of the examples featured in the DOCK Blaster paper (Irwin et al., J Med Chem, 2009, in press, please consult the [[DOCK Blaster:Sample_Data | sample data]].
| | The automatic pipeline to run docking is "dockopt", which is part of [[DOCK3.8:Pydock3 | pydock3]] |
|
| |
|
| = Preparation =
| | The website that allows free public preparation of receptors for docking is called "dockopt". |
|
| |
|
| * [[DOCK Blaster:Preliminaries | Before you begin]]
| | [[Category:DOCK 3.8]] |
| | |
| * [[DOCK Blaster:Prepare Input | Prepare Input ]]
| |
| ** [[DOCK Blaster:Prepare Receptor | Prepare Receptor]]
| |
| ** [[DOCK Blaster:Prepare Ligand | Prepare Ligand]]
| |
| ** [[DOCK Blaster:Other Input Options | Other Input Options]]
| |
| ** [[DOCK Blaster:Input Troubleshooting | Input Troubleshooting]]
| |
| | |
| = Calculation =
| |
| * [[DOCK Blaster:Job Management | Job Management]]
| |
| * [[DOCK Blaster:Results | Results ]]
| |
| ** [[DOCK Blaster:Initial Evaluation | Initial Evaluation]]
| |
| ** [[DOCK Blaster:Results Browser | Results Browser]]
| |
| ** [[DOCK Blaster:Large Database Docking | Large Database Docking]]
| |
| ** [[DOCK Blaster:Custom Database | Custom Database]]
| |
| * [[DOCK Blaster:Technical Details | Technical Details]] of the calculation
| |
| | |
| = Interpretation =
| |
| * [[DOCK Blaster:Acquiring Compounds | Acquire Compounds]]
| |
| * [[DOCK Blaster:Test Compounds | Test Compounds]]
| |
| | |
| = Other topics =
| |
| * [[DOCK Blaster:Philosophy | Philosophy]]
| |
| * [[DOCK Blaster:Annotations | Annotations ]]
| |
| * [[DOCK Blaster:History | History ]]
| |
| * [[DOCK Blaster:Credits | Credits]]
| |
| | |
| To cite DOCK Blaster, please reference Irwin, Shoichet, Mysinger et al., "Automated docking screens: a feasibility study", J Med Chem (2009), in press.
| |
| | |
| = Help =
| |
| For help with DOCK Blaster, please join and write to the DOCK Blaster mailing lists
| |
| [http://blur.compbio.ucsf.edu/mailman/listinfo/blaster-fans blaster-fans at docking.org]. We welcome your feedback about DOCK Blaster. Please send bug reports
| |
| to support at docking.org. Please send opinions to comments at docking.org.
| |
| | |
| = Versions =
| |
| The current version is 1.0.1, released August 6, 2009.
| |
| | |
| Work on DOCK Blaster began in the fall of 2000. The first web-based interface became available inside the lab in 2003. Selective pre-alpha testing started in 2006, alpha testing with external users in 2007, and wide-spread beta testing in 2008. For more info, please see [[DOCK Blaster:History]].
| |
| | |
| [[Category:DOCK Blaster]]
| |
| [[Category:Portal]]
| |