DOCK Blaster: Difference between revisions

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[[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 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 [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].
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.


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"


The automatic pipeline to run docking is "dockopt", which is part of [[DOCK3.8:Pydock3 | pydock3]]


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 [[DOCK Blaster:Sample_Data | sample data]].
The website that allows free public preparation of receptors for docking is called "dockopt".  


= Preparation =
[[Category:DOCK 3.8]]
 
* [[DOCK Blaster:Preliminaries | Before you begin]]
 
* [[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 et al., "Benchmarking Sets for Molecular Docking", manuscript in preparation.
 
= 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]. 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 =
Work on DOCK Blaster began in the fall of 2000.  The first web-based interface became available locally in 2003. We started selective pre-alpha testing in 2006, alpha testing with external users in 2007, and wide-spread beta testing in 2008.
 
DOCK Blaster 1.0 will be released when the paper is published in 2009.
 
[[Category:DOCK Blaster]]
[[Category:Portal]]

Latest revision as of 22:07, 16 September 2022

DOCK Blaster is a program that does automatic docking.

The first version of DOCK Blaster appeared in 2009. Please see Category:DOCK_Blaster

A re-write of the idea of DOCK Blaster, blastermaster.py, was part of the DOCK 3.7 release in 2012.

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

There is also

  • cheminftools - various tools.

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.

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"

The automatic pipeline to run docking is "dockopt", which is part of pydock3

The website that allows free public preparation of receptors for docking is called "dockopt".

Retrieved from "http://wiki.docking.org/index.php?title=DOCK_Blaster&oldid=14819"