DOCK Blaster: Difference between revisions

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DOCK Blaster is a program that does automatic docking.


[[Image:Dblogo.png|thumb|right|DOCK Blaster]]
The first version of DOCK Blaster appeared in 2009. Please see [https://wiki.docking.org/index.php/Category:DOCK_Blaster Category:DOCK_Blaster]


DOCK Blaster is a free-to-use service for running docking screens, on the web at [http://blaster.docking.org http://blaster.docking.org]. You will need at least:
A re-write of the idea of DOCK Blaster, blastermaster.py, was part of the [[DOCK 3.7]] release in 2012.  


* The structure of the target in PDB format (preferred) or mol2 format
In 2022 there were major developments.  First, we reorganized the DOCK repo into three repos:
* A specification of the binding site, which may be one of:
* dock3 - the fortran source code and not much else
** A docked ligand in mol2 format, which is also used to test the docking parameterization
* pydock3 - all the scripts to run docking except for 3d ligand building
** "hot spots", in PDB format, which may be based on one or more ligands.
* ligdock3 - 3d ligand building pipeline
** Atoms of residues forming the binding site. The center of inertia of these atoms should coincide with where you expect the ligand to go.


{{TOCright}}
There is also
* cheminftools - various tools.


That's really all you need to get started. If the target you wish to screen is already in the PDB, you may simply specify its PDB code, and DOCK Blaster will attempt to do the rest.
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.  


If you do not have a particular project in mind, and you are just curious about DOCK Blaster, you can simply use the "I'm feeling lucky" option, and we will pick a target for you.
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"


If you would like to try one of the examples featured in our forthcoming paper, take a look at the [[DOCK Blaster:Sample_Data | sample data]] to experiment.
The automatic pipeline to run docking is "dockopt", which is part of [[DOCK3.8:Pydock3 | pydock3]]


To learn more about DOCK Blaster, please consult the topics below.
The website that allows free public preparation of receptors for docking is called "dockopt".  


== Before you get started ==
[[Category:DOCK 3.8]]
* [[DOCK Blaster:Preliminaries]]
 
== Preparation and Docking ==
* [[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]]
* [[DOCK Blaster:Job Management | Job Management]]
 
== Understanding the Results ==
* [[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:Test Compounds | Test Compounds]]
 
== Other information ==
* [[DOCK Blaster:Philosophy | Philosophy]]
* [[DOCK Blaster:Annotations | Annotations  ]]
* [[DOCK Blaster:History | History ]]
* [[DOCK Blaster:Credits | Credits]]
* [[Terms And Conditions]]
* [[Just Watching]]
* [[Blaster Issues]]
 
 
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
[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.
 
[[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"