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 http://blaster.docking.org].
DOCK Blaster is a program that does automatic docking.  


To get started, you will need at the very least the following:
The first version of DOCK Blaster appeared in 2009. Please see [https://wiki.docking.org/index.php/Category:DOCK_Blaster Category:DOCK_Blaster]
* The structure of the target in PDB format (best) or mol2 format
* A specification of the binding site. This may be one of the following:
** 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]] to experiment. To read more, please consult the topics below.
A re-write of the idea of DOCK Blaster, blastermaster.py, was part of the [[DOCK 3.7]] release in 2012.  


== Before you get started ==
In 2022 there were major developments.  First, we reorganized the DOCK repo into three repos:
* [[DOCK Blaster:Preliminaries]]
* 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


== Preparation and Docking ==
There is also
* [[DOCK Blaster:Prepare Input]]
* cheminftools - various tools.
** [[DOCK Blaster:Prepare Receptor]]
** [[DOCK Blaster:Prepare Ligand]]
** [[DOCK Blaster:Other Input Options]]
** [[DOCK Blaster:Input Troubleshooting]]
* [[DOCK Blaster:Job Management]]


== Understanding the Results ==
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.
* [[DOCK Blaster:Results]]
** [[DOCK Blaster:Initial Evaluation]]
** [[DOCK Blaster:Results Browser]]
** [[DOCK Blaster:Large Database Docking]]
** [[DOCK Blaster:Custom Database]]
** [[DOCK Blaster:Test Compounds]]


== Other information ==
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"
* [[DOCK Blaster:Philosophy]]
* [[DOCK Blaster:Annotations]]
* [[DOCK Blaster:History]]
* [[DOCK Blaster:Credits]]
* [[Terms And Conditions]]


To cite DOCK Blaster, please reference Huang, Shoichet, Irwin, "Benchmarking Sets for Molecular Docking", J Med Chem 2006, 49(23), 6789-6801
The automatic pipeline to run docking is "dockopt", which is part of [[DOCK3.8:Pydock3 | pydock3]]


We welcome your feedback about DOCK Blaster. Please write to us at comments at docking.org.
The website that allows free public preparation of receptors for docking is called "dockopt".  
 
[[Category:DOCK 3.8]]

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"